RobotDan, believe me when I say that to get real multiple-category exclusions -- as opposed to the way that I deal with multiple exclusions whereby, if you want to exclude multiple categories you will only be excluding categories (e.g. you can't do 1 and 3 and 5 but not if they are also in 2 or 4 or 6) -- you are in for a long and frustrating road.
I tried it at one point and gave up. It's not for lack of PHP or MySQL knowledge, I just don't think it can be done using MySQL 4.0. Here's what I said on the wp-hackers list when I finally gave up... might mean nothing to you, might mean a lot, but it will give you some idea of the battle you face:
"I admit defeat... I can't get a clean query to save my life. I can only get a query which would theoretically work by using temporary tables as I was fearing. Using that temporary table and the subsequent goofy $whichcat and $join clauses that result break everything else that deals with those clauses. The general gist of the problem is that you can't simply perform a nice binary logical operation to get the needed rows. Well, you could if you could use a subquery with NOT EXISTS, but we want to be nice to the 4.0 MySQL users and so subqueries are out. Why? Because with exclusions you want only post IDs which have _no rows_ that contain an excluded category. Try doing that with a simple AND NOT clause."