I have most of the Jag releases and enjoy the system quite a bit. I've also had 3DO systems for almost as long, having purchased both around 1995, and have a similar number of games for it (~70, I think). I get a kick out of both systems. The big benefits from the Jag (for me) are the titles that were either Jag-only or had their best versions on it, the fact that there is still active development, and the community on this site and others. I've also enjoyed networked games, although mostly at conventions; if you don't have contact with other Jaguar owners, this isn't a selling point.
The 3DO has some very fun games, including some exclusives and "best version" titles (and its share of mediocre ones and dogs, like any system), but there's nothing new coming for it [some developers claim otherwise, but I haven't seen product]. I also haven't found any communities that actively support it; there used to be good websites like Erin Fritz's, and Usenet was fine before porn spam took over, but active discussion is now hard to find. It's library is much larger, though, and games are generally cheaper... you may want to get the 3DO first. Japanese titles generally work just fine, too... kanji capabilities affect some games, I think, and some others may use the MPEG add-on, but it is good system for dabbling in foreign games. Just call the "CD-R backups" what they are: pirated intellectual property. Anyone with a defensible right to a "back-up" doesn't need one: they have functional original media that will probably outlast the CD-R anyway. I guess I'm just not a warez guy... sorry if I'm overly grumpy about that.
There are several threads on AA covering 3DO and Jaguar game recommendations. You should check them out.
Oh, and if you look at the right (wrong?) 3DO games, you _will_ see "that stupid, blocky, polygon crap." Blocky isn't always bad, though... whether on the 3DO, Jaguar, or VCS
-Mad Scientist