I can't comment on this with respect to windows, but I've been using mod_perl 1.99_09 (Apache 2.0.47/Solaris 2.9/MySQL 4.0.15) at work for quite a while without any problems. (Before anyone jumps on me for not being quite up to date - these servers are on a private network, so security isn't a huge concern.) Performance is good, though my load is few, but relatively intense queries, and your mileage may vary. My understanding is that Apache 2 is worlds better than 1.x on Windows and if you go that route, you have to use mod_perl 2.0 (well, 1.99_12 as of this writing).

Good luck