As with any OS upgrade, we should try to determine if we have any apps that won't run after the update. The previously linked Roaring Apps site will help a bit, but it may best to contact the developer's site for especially critical updates, if they haven't notified you by now.
I just read a report that states that the way
El Capitan handles incompatible apps is similar to how
Yosemite did it with some added capabilities and storage sites.
If the new OS determines the app is incompatible, it will still be in your "Applications" directory but its icon will have the international 'do not enter' (circle with a diagonal line) on it. This also means it should not run even if you try to force it to open.
If it finds plugins/terminal commands or scripts/minor code pieces that are incompatible, it may leave the rest of the app looking like it will be normal. However, those missing pieces may not cause any problems until days/weeks/months after you use that app. You will probably need to do a little searching of your root drive to determine if this has happened. All you need do is open your root drive (often labeled "Macintosh HD") and look for any folders labeled "Disabled Software". Just another reason to double-check with the developer before upgrading the OS.
Lastly, the new Security Integrity Protection function will also look for any code that does not comply with it's rules. Its path is a little lengthy: Macintosh HD (or whatever you might have changed the name to)/Library/SystemMigration/History/Migration-UUID/QuarantineRoot. Most of us will probably never see ing thing here unless you do some kind of app development or use a lot of Terminal/Unix 'tricks'.
The whole point is to know before you jump out of the aircraft that you have a good chute!
Check with any dev that hasn't already told you that their app(s) are compatible with
El Capitan . OTOH, if you notice apps missing from your Dock or Applications folder or they don't do what you expected, try looking in the two places mentioned before buying a Windows machine out of despair or other rash actions!
BTW, we paranoid types would greatly appreciate a posting from you if you come across any problems that might cause any of the above. Please. Help your fellow TSer, even if you're usually only a 'lurker'.