I've done some reasearch on the web and I'm now pretty sure that the 
increased CPU heat only applies to laptops with AMD or Intel chips. 
Something to do with a HLT instruction which has been around for some 
time.  I got this info from the following links -

http://grassomusic.de/english/amdk7.htm 
(Details more than anyone could possibly ever want to know about it!)

http://www.tomshardware.com/mobile/20030102/compaq_evo_n1015v-01.html
(a smaller summary)

http://www.microsoft.com/downloads/details.aspx?FamilyID=2898f8dd-10f8-
4107-9f7b-16c5a525de1e&displaylang=en

That last one just explains that the software side of things is catered 
for in Windows XP.  I also saw fixes for Linux to cater for the HLT 
instruction.

Maybe laptops with other processors do something similar but I don't have 
access to any of those so I'm not too interested.

So I think the SETI FAQ reply is accurate since most computers are not 
laptops.  Although thinking about it - the reply doesn't really relate to 
the question - the question is something along the lines of "Will running 
SETI blow up my computer".  The reply is "No" but then it goes on to talk 
about "additional strain" which is another matter.

The only other possibility is that some chip & OS manufactuers have 
thrown this functionality into their non laptop computers without making 
it clear - though I really doubt that.

Peter