The solution I use to monitor temperature on my MacBook (I run some heavy hour-long processes) is the following:

http://www.increw.org/downloads/speedit.html

Which allows one to use a command line tool to get CPU temp.

http://projects.tynsoe.org/en/geektool/

Where you can have the output from the relevant command displayed in a small transparent window anywhere on one's deskop and have it update every 10 secs.

Works a dream.

Cheers, James