I’ve still not done much with an actual install of El Capitan, though I have it on an old MacBook Pro for testing. I have been working on some back-end things to make sure that machines using my Munki service should upgrade OK, and I think I’m about there – a test install of Yosemite with packages like Symantec EndPoint, Latex, etc upgraded OK, though with various caveats.

• You need to be running MacTeX 2015 for a smooth update due to restrictions on what can be installed in the ‘unix’ directories under El Cap.
• Symantec had an update for SEP out within a few days, and that seems OK. On my Munki service I have set things so the update is only pushed to machines running El Cap as the previous version seems to be fine on Yosemite, and I don’t see the point in fixing what ain’t broke.
• MS Office 2016 seems to be badly broken, and according to Microsoft the fixes will be coming from Apple in an OS X update. How much this affects you depends on how much you use Office. Me – not at all.
• MacPorts has been updated and supports El Cap, though as always a reinstall of all ports is needed for a major OS update.
• IDL 8.5 seems to be OK, though it does not officially support El Cap.
• Ureka (IRAF) already explicitly supports El Cap in the latest release – 1.5.2.
• X11 seems OK under xquartz 2.77 but 2.78 seems close to release with some bug fixes.

At the moment I still don’t recommend installing El Cap on a ‘work’ machine which you can’t afford to lose. Maybe once 10.11.1 is out – though I have some new incoming Macs which I assume will ship with El Cap now, so they’ll be ‘volunteering’ to test.