We have been deploying ArcGIS Desktop via Citrix since Desktop v8.3, with pretty good success. Our active user base is 500+. Our most frequent issues have been with corrupted terminal services profiles, due to any number of causes.
Desktop v10 assumes even greater use of profiles, for storing geoprocessing log files, the default home workspace, and most significantly, the default gdb and image caching for basemaps.
If anyone else has encountered this issue, and resolved it, I would be very interested in hearing from you.