I have both. The first thing is that with the desktop version you have to be careful of the height of the RAM that you get for it. The RAM from OWC says it will fit, but it's actually just a mm or 2 too tall for the computer. This isn't a problem with the mini tower. I think the drives bays are easier to get at in the desktop, but the mini tower is a full 100 MHz faster and feels a bit snappier to me. Definitely check for which personality card is in the machine. One will be 1/8" audio in and out only, while another is A/V in-out with S-Video and Composite in-out, and for audio: 1/8" and RCA in and out.
Either of these make great 'translation engines' or 'puddle jumpers' as they have Floppy, zips, IDE and SCSI along with your above mentioned Serial ports. Add a PCI firewire card for cheap if you have a firewire drive. I have yet to get USB nor SATA working on one, but a super cheap IDE to compact flash adapter is simple plug and play. Oh, and both have built in Ethernet. add a cheap WIFI bridge, and call it a day.
I love the Beige G3's =)