Off the top of my head MS Office, Adobe Fireworks, and a load of games.
They mostly all relate to OSX switching to Intel processors with isn't to different to Windows switching to ARM. Leopard would support PowerPC apps through Rosetta. Snow Leopard then removed Rosetta and you had to install it manually to get your Power PC apps to run. Lion then dropped all support completely.
Aside from intel switchover though I've had full screen games that no longer work relating to differences in graphics cards when you get a new machines. And there is just software that doesn't work following OS upgrades, this site and Mac Rumors tend to publish an article around the time listing known issues.
It's completely unavoidable. You either make the OS completely bloated by trying to make everything work or force people to update there software with there OS. The same as if people want a low powered processor there going to need software that can run on it.. The Windows 8 metro apps actually make the situation slightly better as there (mostly) an extra layer of abstraction away from the processor they don't need to be recompiled for each processer.