The first thing that struck me is how much less important the OS is when compared to the situation a few years ago: a lot of the applications I depend on are web-based (GMail, Google Calendar, Google Docs, Springpad), and the ones that are not web-based are multiplatform and installable with a few clicks (GVim comes to mind). In fact, I do not think there is a single piece of software that I really missed in Windows. (An interesting corollary of this observation is that it should be equally easy to migrate to GNU/Linux nowadays.)
The one thing where the operating system matters is hardware support, and I do not think I have to say much here. After years of whack-a-mole GNU/Linux upgrades which would fix support for one component but break another (for things as essential as video and sound), it was absolutely weird having all hardware work properly at the same time (sound after suspend! no video glitches! high quality webcam picture!). There is no point recounting the reasons why hardware support in Linux is as it is, but now I am starting to think that Linux users do tend to suffer from a sort of Stockholm syndrome regarding hardware support; I know I did.
The other important thing that operating systems do is resource management, and I did not have problems here either. In fact, I liked the virtual memory behaviour much better: when Windows ran out of memory (I had filled up the smallish Windows partition and there was no space left for the swap file to grow), it started rejecting malloc calls from applications, but the system was kept alive and responsive, and I could close apps and clean up the mess without much trouble. In Ubuntu, with the default settings, whenever a runaway process ate too much RAM, the system would start thrashing so hard that it would be very difficult to fix. My standard procedure (switch to text console, log in, find and kill app using command line tools) would take minutes and was so annoying that I would sometimes just reset the computer instead. And in the end, even if I did not reset, an important app would possibly be killed anyway. I know there are kernel parameters for tweaking this behaviour (swappiness?), but I never got around to figuring them out as this situation does not arise that frequently, and testing is painful.
I did not like the Windows FS security model. ACLs are much more complicated and thus less transparent that the Unix approach, even though they are more powerful. My main gripe with them is that I do not know a good way to display them easily (as with ls -l in Unix). I have not had to deal with them much though.