yo snagglepus, no need to feel stupid its a very valid question
one of the problems with most toplists, and link exchange scripts is there use of redirection to count hits in and out, your right this doesnt not bode well with the likes of yahoo and google.
One solution to this is scripts that count hits IN based on the refer value. This mean people can link directly to
www.yourdomain.com and almost all hits IN will still be counted. This works well for search engines who would award the full value of the link to your domain.
One such script is cjoverkill which is free but will skim 1% of your traffic i believe, while its not traditionally a toplist it has all the features you need to set one up.
Or if youve got money to burn a believe the UCJ works in a similar way as well.
One thing you will need to consider tho, is that many site linking to you, might well be using thier own link exhange scripts and thus wont be linking directy to you, but redirecting to you through thier script, for this links the Search engine value will be diminished.