You'll still need an Orinoco (or comatible) card for MiniStumbler. It's basically the same as NetStumbler just tweaked (seriously tweaked

for the smaller computer.
I haven't done GPS.
Audible alerts are there - just put a sound file named ir_begin in the same directory that ministrumbler is in.
No personal experiece with your mapping/gps questions.
There is a linux build for the ipaq and there's a jave sniffer for that. There is a CEsniffer for the Ipaq that works really well. It costs $249 I believe. That somewhat addresses your 'other tools' question.