##El Capitan Applications Issues##
El Capitan has incompatible Applications List: /System/Library/PrivateFrameworks/SystemMigration.framework/Resources/MigrationIncompatibleApplicationsList.plist (Rich Trouton)
VMware View - 3.4.1 works in El Capitan (JHUAPL & AnswerWare)
IBMNotes - does not work in El Capitan - "fix coming in the autumn" (Jennifer Unger)
Wi-Fi/802.1X - Make sure you have Diffie Hellman keys with a group size of 2048 bits or LARGER, otherwise things may be problematic in iOS 9 & El Cap
##Display Adapter Issues##
Display adapters that do work - normal dvi and normal dvi. Duallink - no for some hardware. Apple changed EDID Handshake, so watch your displays. (Dan Griggs)
4K TVs and Iris Pro, all the clients failing (AnswerWare)
##System Integrity Protection##
HT205054 - KBase article for Bless & SIP - You may want to reconsider PRAM Zaps "There are ways to manage SIP" - Apple Enterprise Support may help you. Once it ships. Maybe. You might have to sign an NDA. (Rich Trouton)
Anything with unsigned kernel extensions, things in protected directories, and some vendors are going to say "Turn off SIP." Anyone telling you to turn off SIP is not your friend. Demand better from your vendors.
XProtect is no longer manageable, because of SIP, so be aware and be prepared to handle that
##Apple's SIP Guide for El Capitan##
Apple's Developer Guide (Rich Trouton)
##Issues with Extreme Z-IP/Access Connect##
Icon Previews & Lists when browsing server. Used to be viewport content only, but now is not limited to visible files. Would sometimes continue when all the Finder windows are closed and all data has arrived. Apple is looking for customers for a bug's breadth. They fix bugs based on the number of affected users in some cases.
Apple can help you quantify that affected users data. Have a good relationship with your SE.
AFP Network Home Directories Busted? There are challenges here. Test.
##AirPlay##
Third party apps may not be updated for AirPlay Integrations. Pay close attention to your third parties. Reflector just updated, so did AirServer. Check to make sure it works.
##iOS 9 Issues##
If you're running Good for Enterprise, you HAVE to upgrade to Good 3.1.0 Client before you upgrade iOS 9. Otherwise, you can't just update the app binary, you have to uninstall, reinstall, re-enroll. (JHUAPL)
##Other Cool Tips:##
Plug in iOS 8+ Device, open QuickTime Player, get to choose the device. Now you have a local reflector!
Apple has been rolling their whitepapers into the OS X and iOS Deployment Reference Guides.