Walter Randelshofer's Pretty Patterns collection (for Rubik's cubes up to 5x5x5) is one of the nicest twisty puzzle sites going. It's based on his CubeTwister software, which you can download (including a lovely OS X standalone). If you really want a treasure trove of twisty polyhedra, check out gelatinBrain's enormous collection of java applets (which unfortunately don't do so well on macs). Are those things even physically possible? Really? Mini bonus: Randelshofer also hosts an archive of fondly-remembered Amiga animations.
Top 10 Google Tools you forgot all about. Though some of these (Google Books, Google Trends and Google Base) have been mentioned a few times on MeFi, there are still some diamonds in the rough like Google Alerts, Google Code search, Google Notebook, Google's latest/experiment ideas and Flight Simulator in Google Earth.
Jigzone - Another great place to waste time at work. The page features a java applet that lets you put together different jigsaw puzzles. I just started working tech support this week and the first day the person that was training me told me about this site. So far it has saved my sanity many a time.
fun with faces. using applets, ken perlin built an interactive facial-expression thingy. i found this site because ken is responsible for the cute lil heart animation at google. there are quite a few interesting thingamabobs to check out at his site.
S u m e a features some amazing ways to use Java and Flash on the web. The best thing about the whole site is how fast all the 'applets' load on my 56k modem.