I was using that CityID app (bloatware) that came with the stock phone. Normally I would never pay a monthly fee for something like that, but work pays for my phone and it was useful to see the city/state of the caller, so I was using it. But it's not compatible with this ROM - though I doubt more than .001% of people would care about that.
ADWNotifier also seems to have issues, but that really wasn't much of a concern either.
I also can't seem to get Face Unlock working, but I really wasn't planning on using it, just playing around with it. Unless my phone is idle for >30minutes, I just use a third party slider app to jump directly to certain applications anyway.
So all in all, a few minor inconveniences, but nothing that would make me really care about the loss. Everything else works perfect and faster. Also, if you do go with that ROM, make sure you install the better Fluxi kernel afterwards:
http://forum.xda-developers.com/showthread.php?t=1664688
I did run into one hiccup during installation - make sure you reboot it AGAIN right after it boots into the ROM for the first time. Otherwise your APN settings might not be showing properly. Rebooting will fix this.