In no particular order

• “Put-back” from Trash is not available >50% of the time
• Cut-paste does not exist - moving files is painful; drag-drop is no solution, since the windows dance around uncontrollably.
• Needing to buy software, find hacks, or create hacks to fix these things which should work properly out-of-the-box
• No Winamp alternative (cmus via homebrew comes closest)
• region locked dvd player
• no mode configuration for wireless adapter
• unofficial package managers, and outdated versions of gcc & other essential tools

Though on the other hand I will miss:

• killer apps, such as the Omni products, Smartr, .. actually I’ve been weening myself off mac apps lately so I’m not too worried about this
• it-just-works drag-and-drop support. It’s hard to explain this to non-mac users. Basically when you drag-and-drop an application (unless badly written, e.g. Mendeley desktop client) will do what you want it to do, rather than something stupid
• it-just-works in general, when it does
• Keyboard shortcuts. I’ve been using Windows through VMware Fusion, and text editing in MS Word HURTS. I need to find a fix for that fast, though will mostly be working in Linux where it should be fine.
• the cosmetics (fonts, desktop wallpapers, etc)

It’s going to be interesting switching back.