Hard drives are hard drives, as they say. True plug and play with firewire and usb. Modern Macs' HD's are formatted HFS+. However, they can also read/write FAT32 and as of OS X 10.4 (Tiger), can read NTFS. I have an NTFS external firewire/usb drive that I use whenever I need to go get a bunch of files from an XP box (or ship it as I have with some ot.com members for their video captures). I'm not sure about partitioning different formats on the same drive, if that would work or not. I know from experience that although you can format a drive FAT32 within OS X, it works better if it's formatted on a PC and then read on a Mac.

So,

HFS+ (mac native disk format, only bootable mac format)
FAT32 (mac read/write, no boot) most off the shelf external firewire/usb2 hard drives are pre-formatted FAT32. A Mac can read/write just as easily as a PC.
NTFS (mac read only, OS X 10.4 Tiger only)

Also for GundarkHunter,

I believe the mac mini's built in HD is 2.5 inch 4200rpm (someone correct me if I'm wrong). This really wouldn't be suitable for running a real video editing app (ala Final Cut Pro). A great option would be something like the NewerTech miniStack. It has the same form factor as the mini and sits directly underneath it. You can get it with or without a 3.5 inch drive. What I would do is put a big (200-500 GB) 7200rpm drive in there and use it as your boot drive hooked up to the mini via firewire (you probably have an extra few of these lying around). This would give you much better performance. Heck, I'm able to run Final Cut Pro on a 3 year old 1GHz iMac G4. So, the G4 is fine you just need a much faster hard disk than the mini's. If needed, you could always daisy chain mulitple miniStack's or any other external disks. With this setup, I would just use the mini's hard drive for storage (photos, mp3's, whatever).

I'm glad to see more people making a switch. The grass really is greener over here! (and has been for a long time)