I have been using my upgraded Mac Mini (Core Single to Core 2 Duo Upgrade) for almost two weeks now. So far I did not experience any crashes or similar things but as I wrote earlier I was not very happy with the heat.
In addition I noticed that the fan did not speed up (it stay around 1600rpm all the time), if the cpu was extensively used, and speed stepping of the cpu (Intel Enhanced Speedstep) did not work. In the apfeltalk.de-Forum I got the hint to reset the PMU and to update the Mac Mini’s firmware. After doing so the fan speeds up on high load and the maximum temperature dropped from 97° celsius to 90°. Not very much, but hey….it’s a good start. 
Unfortunately speed stepping of the Core 2 Duo still does not work properly. The cpu frequency decreases to 1 Ghz but increases back to 2 Ghz within a second. If anyone has a hint…please drop me an email.
Here are some values and graphs from Hardware Monitor:
Normal load (screenshot done after 2 hours of using Firefox, AdiumX, NetNewsWire Pro, EyeTV, Skype):
Maximum load:
cpu speed stepping:
i have the same problem and solved it with smcfancontrol or for professional use you should try coolbook, but if you are and expert cause using this app withut voltage and mhz knowledge will crash your mac…