There are problems with some GNU projects that rely on case-sensitivity. When Apple introduced the new format, they didn't push it, but using it (I did, because I thought it just sounded "better", although I didn't intend to start naming my files the same but in different case) revealed problems with a couple of applications. Adobe CS 2 applications didn't want to start (they died on launch), neither did Fetch at the time and a couple more.
I'd say most projects, by now, know about Mac OS X' ability to run on a case-sensitive OS.
If anything, after going case-sensitive, doesn't want to launch, you can do the following, a workaround I found out back then for Adobe's apps: Create a case-insensitive disk image (auto-growing) and put the apps that don't want to launch in there. Just keep that mounted at all time. The apps will launch.