Percentage wise compatibiltity is pretty good, unfortunately the few percent that do not work consist of the GBA's finest.
Of course anything I say is subjective so I will present you with a trusted list with which you can make up your own mind:
http://rothmans.joskeonline.com/supercardsite/
Supercard DS compatibility (pretty much the same for all big manufacturers cart regardless what the 900 moaning threads say, especially if you wait for a few days after a non working release):
http://www.dualscene.net/viewpage.php?page_id=28
Homebrew wise the supercard is supported very well although between 3rd party developers and the companies that make carts releasing libraries/sources other carts are doing pretty good too, not to mention a load of homebrew continues to use the GBFS (Gameboy file system) which will work on nearly all GBA carts around.