I experienced frustrating glitches in various programs, including Microsoft Word, Flip4Mac, Photoshop CS3, CyberDuck and TextExpander, an abbreviation expander. (Interestingly, Snow Leopard offers its own typing-expander feature, but it works primarily in Apple programs, like TextEdit, Mail, Safari and iChat.) The compatibility list at snowleopard.wikidot.com lists other programs that may have trouble.
Most of these hiccups will go away when software companies update their wares (although Adobe says, Just upgrade to Photoshop CS4). Lets hope that Apple hurries up with its inevitable 10.6.0.1 update, too, to address the occasional Safari crash and cosmetic glitch I experienced, too.