I am trying to identify Mac apps which people use which are not (exclusively) in the Mac App Store. Please add suggestions in the comments. I came up with almost 100 but I am sure that I am missing some. Any help appreciated.

3rd Party Mac Apps.txt

 1 1Password
 2 Accordance
 3 Alfred
 4 Appfixer
 5 Arqbackup
 6 Audiobook Builder
 7 Audio Hijack
 8 Bartender
 9 Battery Alert
10 BBedit
11 Beamer
12 BitTorrentSync
13 Busy Cal
14 Busy Contacts
15 Calibre
16 Carbon Copy Cloner
17 Charles
18 Choosy
19 Clarify
20 Cloak
21 Cocoa Packet Analyzer
22 Coda
23 Code Runner
24 Daisy Disk
25 Default Folder X
26 Desktop Curtain
27 Detect X
28 DevonTHINK
29 Downie
30 Dropbox
31 Duet Display
32 Endurance
33 Evernote
34 Expandrive
35 Fantastical
36 Feeder
37 Fission
38 Flash
39 Flux
40 Foreversave
41 Gemini
42 Github
43 Handbrake
44 Hazel
45 Hocusfocus
46 Imageoptim
47 iTerm
48 Itsycal
49 Jettison
50 Kaleidoscope
51 Karabiner
52 Keeping You Awake
53 Keyboard Maestro
54 Knock
55 Launchcontrol
56 Liteicon
57 LittleSnitch
58 Logos
59 m4vgear
60 Macpilot
61 Mailmate
62 Mailplane
63 Makemkv
64 Marked
65 Marked 2
66 Marsedit
67 Mountain
68 Namemangler
69 Netspot
70 nvALT
71 Office
72 OmniDiskSweeper
73 OmniFocus
74 OmniGraffle
75 OmniOutliner
76 OmniPlan
77 PathFinder
78 PDFpenPro
79 Printopia
80 Quitter
81 Resolutionator
82 Revisions
83 Scrivener
84 Seil
85 Shortcat
86 Slack
87 Spectacle
88 SSH Tunnelmanager
89 Subtitles
90 SuperDuper
91 Task Paper3
92 Textbar
93 Textexpander
94 Tower
95 Transmission
96 Vellum
97 VLC
98 XQuartz

Here are a few I can recall (trying not to repeat myself, but if something slips through...do forgive 😄 ) :

1. Airmail
2. Boom 2
3. ChronoSync
4. CleanMyMac
5. Code Runner
6. Contexts
7. Control Plane
8. Dropshare
9. Dropzone 3
10. Enpass (Enpass.io)
11. Entropy
12. Forklift
13. Franz
14. HoudahSpot
15. iStat Menus
16. LaunchBar
17. MoneyWiz
18. Moom
19. PopClip
20. Royal TSX
21. Sketch
22. Spillo
23. Things
24. Transmit
25. Trickster
26. Typinator
27. Virtualbox
28. Yummy FTP Pro
29. All apps by Macphun, Macpaw, Omni Group, Realmac

If there's an AutoPkg recipe for it, it's very likely to be available outside of the App Store.

What's on my own system that hasn't been mentioned.

1. Atom
2. Cyberduck
3. Divvy
4. Espresso
5. Loopback
6. Moneydance
7. Rescue time
8. Soundsoap
9. Stay
10. UnRarX

Power Manager thrives outside the Mac App Store.

Additional software on my machine:

1. AppZapper
2. Backblaze
3. Banktivity
4. CodeKit
5. Firefox
6. TransType

1. Airfoil

Records for Mac - www.records.team

You didn't specify "exclusively" out side the App Store or just available outside the App Store at all, but here are a few not listed in your list above:

Acorn
Blender
Coda
Colloquy
Cornerstone
Google Chrome
Little Snitch
Reveal
Scrivener
Skype
SourceTree
Steam
Unity

A bit on the nerdy side, but Sequel Pro's still a downloadable application. http://www.sequelpro.com/

As I mentioned you at TT – all Adobe apps:

Photoshop
InDesign
Illustrator
Acrobat
Bridge
Premiere Pro
After Effects
Audition
Dreamweaver
Prelude
Muse
Lightroom

1. Data Rescue
2. DiskWarrior
3. GrandPerspective
4. GrandTotal
5. Shimo
6. VMware Fusion