I've spent a lot of time on my Mac computer and these are the things I use to make it the way it is.

Mac Stuff

List of free mac things to make it better
These are what I like. There are more than one things that do the same thing and here I only list one probs. These work for me but may not for you. 
This is designed to make new machines usable, and simplify the process of restoring old ones. 
Install things in this order, unless you don't want to. 
You can skip stuff, I don't really care. I'm a text file, not the police.

----------------------------------------------------------First step(big stuff)-------------------------------------------------

Xcode(For coding stuff, really big though.)
https://developer.apple.com/xcode/
Xcode command line tools(important!)
\/ \/ Install \/ \/
xcode-select --install
\/ \/ test if working \/ \/
xcode-select -p
gcc --version

Homebrew(osx package manager)
-should already be installed if you ran the other scripts
http://brew.sh/

Cask(Goes with homebrew)
brew install caskroom/cask/brew-cask
https://github.com/caskroom/homebrew-cask

Oh my zsh(Better shell than bash)
http://www.maclife.com/article/columns/terminal_101_better_shell_zsh

Solarized light ansi(Nice theme for terminal)
-might already be installed via oh-my-zsh
https://github.com/altercation/solarized

Osx-for-hackers.sh(Configure your mac a lot better, read through and edit before running though.)
https://gist.github.com/brandonb927/3195465

Laptop(script to set up laptops for development)
-sets up homebrew (I think) (maybe remove that part)
-also zsh? who knows what this will do
https://github.com/thoughtbot/laptop

Rails(ruby on rails! some parts should already be installed)
https://gorails.com/setup/osx/10.10-yosemite

Macports(like homebrew but has some other stuff also)
-should already be installed but it's been kinda tricky in the past
--I had to compile from source
-Don't forget to "sudo port selfupdate"
-you should update commands like man and sudo
--if you want to I mean
http://guide.macports.org

------------------------------------------------Second step(not in app store)--------------------------------------------

Brewfile(is in ~/Documents/Backup, installs a ton of apps at once)(if you're not max I'd recommend skipping this step and manually installing things you want from the "in brewfile" section)(if you are max you should still look through it anyways)
to run-
brew tap homebrew/bundle
cd /directory\ with\ brewfile
brew bundle
tada

Flashlight(If you're into the mac ecosystem)
http://flashlight.nateparrott.com/

Service-Delete Immediately(Delete single file without having to empty whole trash)
https://github.com/jtbandes/delete-immediately

PopcornTime(Streaming torrent client, easy to use)
https://popcorntime.io/

Spark(Keybinds editor, also good for messing with people(e.g. cmd c --> shutdown, no prompt)
http://www.shadowlab.org/Software/spark.php

Spotflux(Pretty good free VPN)
https://spotflux.com/

Archives.prefpane(Activate this to remove zip files once unzipped)
Find this in deeper I think

Suspiciouspackage(Quicklook plugin to examine package contents)
http://www.mothersruin.com/software/SuspiciousPackage/

Simbl(Plugin framework, necessary for safaristand and afloat)(Do not use easysimbl unless it works now, it doesn't as of writing this)
http://www.culater.net/software/SIMBL/SIMBL.php

Afloat(pin cocoa based apps)
http://www.macupdate.com/app/mac/22237/afloat (Sorry for macupdate link!)

Safaristand(Make it so you can stand safari)
http://hetima.com/safaristand/

CustomNC(Customize how notifications work!)(Also needs simbl)
https://github.com/inket/CustomNC

----------------------------------------------2.25th Step(Commands to run)--------------------------------------------
Makes Things Open Faster, appear snappier
Disable opening and closing window animations
defaults write NSGlobalDomain NSAutomaticWindowAnimationsEnabled -bool false
Disable Mission Control Animations
defaults write com.apple.dock expose-animation-duration -int 0
Increase window resize speed for Cocoa applications
defaults write NSGlobalDomain NSWindowResizeTime -float 0.001
Don’t animate opening applications from the Dock
defaults write com.apple.dock launchanim -bool false


----------------------------------------------2.5th step(in apple app store)----------------------------------------------

simplenote(Another good note taking app, cross platform)
http://simplenote.com/

Apple configurator(mange and restore ios devices)
https://itunes.apple.com/us/app/apple-configurator/id434433123?mt=12

Cleanmydrive(Gets rid of hidden deleted but not really files on flash drives, and ejects better than the system sometimes)
http://macpaw.com/cleanmydrive

RAR Extractor free(Works well for extracting RARs, better than unarchiver imo)
https://itunes.apple.com/us/app/rar-extractor-free/id646295438?mt=12

Wontube free video converter(Literally the best video converter ever)(except maybe handbrake)
https://itunes.apple.com/us/app/wontube-free-video-converter/id495101962?mt=12

-----------------------------------------------Step 2.75: 2.75 fast 2.75 furious(Paid apps)---------------------------
These apps are good. 

Bartender(Clean up Menubar)
http://www.macbartender.com/
Price: $15 (A little expensive but it looks p nice)
4 Week Free trial

Control Center(Minimalistic info thingie)(I don't use it but it looks good so it's here)(he's also got a p rad lookin thing called disk sensei)
https://www.cindori.org/software/controlcenter/
Price: $7 but on sale for $5

Disk Sensei(Like disk util but better)(Note:I do not have this)(look up some reviews maybe)
https://www.cindori.org/software/disksensei/
Price: $19.99


----------------------------------------------------Third step (in brewfile)--------------------------------------------------

Google Chrome(Browser that I like)
http://www.google.com/chrome/

thefuck(type "fuck" after some incorrect terminal commands to fix them)
https://github.com/nvbn/thefuck

iTerm2(some people like this, better version of terminal)
http://iterm2.com/

Evernote(Take and save notes, now better than ever!)
https://evernote.com/

Tor(Access onion sites and bypass restrictions)
https://www.torproject.org/

Notational Velocity(one good note taking app)
http://notational.net/

Atom(Really good looking text editor)
https://atom.io/

Bettertouchtool(trackpad shortcuts and window management)
http://www.bettertouchtool.net/
Enable these
-window manager
-2-finger swipe to cmd alt left
-3-finger middle click

Alfred(Better alternative to spotlight)
http://www.alfredapp.com/

Infinit(File sharing)(Blocked on school network)
https://infinit.io/

f.lux(Screen light filter, makes it not have as much blue light at night)
https://justgetflux.com/

AdwareMedic(Pretty much the only good adware remover)
http://www.adwaremedic.com/index.php

Deeper, OnyX, Maintenance(Mac utilities, don't need to do the "run scripts every so often" thing)
http://www.titanium.free.fr/

Gas Mask(Easy host file switcher, good for messing with people and DNS spoofing)
https://github.com/2ndalpha/gasmask

Hex fiend(Hex editor)
http://ridiculousfish.com/hexfiend/

Keeping you awake(One click in finder bar to stop device from sleeping)(better than caffeine)
https://github.com/newmarcel/KeepingYouAwake

Libreoffice(free office suite)
https://www.libreoffice.org/

OpenEmu(One of the best emulators)
http://openemu.org/

Powder(Fun game, you can build things and mess with electronics, or just blow stuff up like most people)
http://powdertoy.co.uk/

Sublime text editor(Text editor a lot of people like)
http://www.sublimetext.com/

Textwrangler(Better than having to open xcode every time you want to edit a config file)
http://www.barebones.com/products/textwrangler/

Transmission(Best torrent client IMO, don't use utorrent)
http://www.transmissionbt.com/

unetbootin(not great at all but is ok for making bootable flash drives)
http://unetbootin.sourceforge.net/

Virtualbox(virtualization sofware)
https://www.virtualbox.org/wiki/Mac%20OS%20X%20build%20instructions

VLC(Media player, somewhat better than qt)
http://www.videolan.org/vlc/download-macosx.html

Wine(Run some windows programs)
http://winebottler.kronenberg.org/

Wireshark(Capture and analyze network traffic)	
https://www.wireshark.org/download.html

Ccleaner(Clean useless files, run maybe once a month(also has other features))
https://www.piriform.com/mac/ccleaner

Disk Drill(Disk analyzer, recover files, SMART monitoring)
http://www.cleverfiles.com/

Gimp(You know what Gimp is)
http://www.gimp.org/

Handbrake(Another media converter, don't know quite how it works but apparently it's good)
https://handbrake.fr/

Hexchat(IRC client I think)
https://hexchat.github.io/

MacUpdate Desktop(see what software is outdated, don't buy it though lol)
http://www.macupdate.com/desktop/

OpenOffice(Another free office software, similar to libreoffice)
https://www.openoffice.org/

Perian(Quicktime playability extender, play more types of files)
http://www.perian.org/

Secrets.prefpane (Run before osx-for-hackers, allows lots of hidden preference changes)
http://secrets.blacktree.com/

Crashplan(I use this for local backups of certain files)
http://www.code42.com/crashplan/

Steam(gaming platform)
http://store.steampowered.com/

Minecraft(a game)
https://minecraft.net/

Mcedit(world editor for minecraft)
http://www.mcedit.net/

Epic Games Launcher(editing unreal engine, unreal tournament)
https://www.unrealengine.com/what-is-unreal-engine-4

Disk Inventory X(see what takes up space)
http://www.derlien.com/

Sdformatter(Formats SD cards)
https://www.sdcard.org/downloads/formatter_4/

Spotify(stream music)
https://www.spotify.com/us/

Etrecheck(find out what's wrong)
http://www.etresoft.com/etrecheck

Audacity(Record directly from computer with soundflower, also some other stuff)
http://audacityteam.org/

Soudflower(for recording things)(they also have some other cool apps, try piezo!)
https://rogueamoeba.com/freebies/soundflower/

Thanks for using this!

Now, how do you update all these homebrew installed apps? Just run "brew update" and then "brew upgrade"!
Or, even simpler, run
brew update && brew upgrade
!

------------------------------------------------π th step(Browser extensions)--------------------------------------------

Safari
 ublock(blocks ads, memory efficient & open source)
https://www.ublock.org/

Chrome
  ublock/ublock origin(blocks ads, memory efficient & open source)
https://www.ublock.org/
https://chrome.google.com/webstore/detail/ublock-origin/cjpalhdlnbpafiamejdnhcphjbkeiagm?hl=en

 Browsec(Get around network blocks, works better than most others)
https://chrome.google.com/webstore/detail/browsec/omghfjlpggmjjaagoclmmobgdodcjboh?hl=en

 The Great Suspender(Save memory on chrome by suspending unused tabs)
https://chrome.google.com/webstore/detail/the-great-suspender/klbibkeccnjlkjkiokjodocebajanakg

Backstop(make delete key not go back in history)
https://chrome.google.com/webstore/detail/backstop/pidcjgldchekcoolelhbjfbnccjkckfj

Chrome Remote Desktop(remote in from phone/other computer)
https://chrome.google.com/webstore/detail/chrome-remote-desktop/gbchcmhmhahfdphkhkmpfmihenigjmpp?hl=en

Evernote Web Clipper(save articles or pieces of text to evernote)
https://chrome.google.com/webstore/detail/evernote-web-clipper/pioclpoplcdbaefihamjohnefbikjilc

Reddit Enhancement Suite(make reddit better like 10x)
http://redditenhancementsuite.com/

Wikiwand(make wikipedia look nice)
http://www.wikiwand.com/

XKit(make tumblr better like 9.5x)
http://www.xkit.info/seven/

----------------------------------------------BONUS ROUND(Android apps)--------------------------------------------
I'm not putting links because it's late and I don't feel like it
I might add them later though
They also are not sorted
I also might do that later

Dropbox(Share Files)
Facebook/Facebook lite(Communicate with people)
Google Translate(Do language Homework)
Facebook messenger(Talk to people)
Netflix(Watch movies)
Shazam(Find out what song is playing)
Skype(Talk to more people)
Snapchat(Send nudes)
Tumblr(idk)
Youtube(Watch videos)
Chrome(Web browser)
Gmail(Check school email)
Drive(Lots of stuff)
Hangouts(Text replacement, is p good)
Maps(Find way)
Smart Remote(Control 95% of tvs)
Greenify(Kill background apps)
Nova launcher(Better launcher imo)
Google Keep(Take notes, make to-do lists)
Moonshine Icon Pack(Nice quasi-material icon pack)
Google Authenticator(2 factor auth for many things(gmail, slack, tumblr, evernote, etc))
Malwarebytes(malware removal tool)
Baconreader(reddit client)
Quizup(Online multiplayer pvp quiz)
Google Messenger(text replacement app)
Chrome Dev(dev version of chrome, have new features NOW!)
Google Inbox(Use for all non-school emails)
Slack(Message people w/ it)
Evernote(Notes)
Shortyz(Crosswords app)
Showbox(popcorntime for android, torrent streaming client)
Spotify(Music)
Play Music(Play audio files)
Iheartradio(tune in to radio)
Quickpic(gallery replacement)
Remote Desktop(Control computer without getting up)
TrueDialer(Dialer replacement)
Twitter(Talk to birds)
Wabbitemu(Graphing calc emulator)
Simplenote(Another note thing)
Automatic Call Recorder(record all calls automatically)(Check if this is legal where you live)
Barcode Scanner(scan some barcodes, qr codes)
Curated(Find games here)
Evernote widget(see evernote on home screen)
Flud(torrent client)
FX File explorer(see files)
Google Keyboard(better keyboard than stock, imo)
Infinit(fie transfer)(works v nice between mac and android)
Muzei(wallpaper changes every day, blur)
Yahoo News Digest(get the news)
Relay(Reddit client)
SD Maid(clean space, also get the pro key)
Secrecy(hide nudes/porn in encrypted containers)
TeslaLED(Flashlight)
Truecaller(know who unknown caller numbers are)
Google Voice(visual voice mail, sometimes takes a while to update)
Vortex(Lightweight twitch client)
Vulcan(voat client)
Zedge(ringtones and shit)