One of the most used gestures I used to use on Snow Leopard was the 4-finger horizontal swipe to change apps. Now, I have to use CMD+TAB..
There is 3rd party hacks that enable this, but they aren't quite the same (for example, in Snow Leopard, a 4-finger swipe left/right then lifting would just switch to that app, something that 3rd party hacks don't automatically select). I don't see why Apple took this functionality away - it works on full screen apps, but you can have it work on windowed apps too without causing issues.
Another one is the Show Desktop gesture. In Snow Leopard, a simple swipe up, something you could do while dragging a file. Now in Lion, it's an awkward gesture that you cannot carry out while dragging a file.
I like some of the iPad "evolved" gestures on Lion, but the Show Desktop one I just can't stand..