I was in the same position a month ago and did a huge amount of research (much thanks to Steve for providing one of the best resources) before I decided on the D60. Without going into detail on why I made my particular decision, both of these cameras are exceptional. The biggest factor you'll likely encounter is previous investments. If you have Nikon lenses, buy the D100. If you have a Canon investment, then the D60 is probably for you. If you have nothing invested as of yet, then the decision becomes much more difficult.
I bought the Canon, and I've had four Nikons in the past. eBay erased my previous investment for me so that I could make a "unbiased" decision
Good luck with your decision. I know you'll enjoy either one.