I'd totally agree with Robbieduncan about the Firewire drive. If you *really* want to see an increase in performance with the mini, grab a 3.5" firewire enclosure, stick any modern 7200 rpm 3.5" desktop hard drive inside, and boot off of that instead. If you're concerned about aesthetics, just get a fairly long firewire cable and tuck the external drive out of sight. That's a cheaper solution with better performance than any other laptop drive you could stick in there. Plus, if you set up the partitions right, you can then use the internal laptop drive as a full bootable backup clone of what's in your external drive, so that at any time you could unplug the external drive and just run off of the internal. Lots of benefits to running this way.
The drawback is having something else plugged into the back of your mini, and perhaps noise if you're a noise freak like me. Desktop drives tend to make more noise than notebook drives (though the samsung and seagate drives are very quiet), and that can take away from one of the main advantages of having the mini in the first place.
Also, if you're going to upgrade the internal drive, you might as well drop the 20-30 bucks on a FW enclosure for it. These are easy to use, and when you're done installing the new drive, you can throw a base install of panther/tiger on it, and then use the other drive to pull the settings over. I've done this about 4 times last week as I've been moving from mini to laptop to laptop, and it's one of the HUGE superiorities of os x over windows. Migrating my complete machine from a mini to a powerbook took a total of about two clicks of a mouse and plugging in a cable, and it all just works! I've never, never been able to do that with windows, and doing it with linux is a lot more hands on as well. You'll save yourself a lot of time. And then the external drive can, once again, be a backup drive for a bootable clone of your current OS or just a place for extra storage.
Here's the macally notebook enclosure I've got. It works great. I picked it up from newegg.
macally notebook FW enclosure
good luck.