I've always thought Syndicate deserves to be closer to the top of the list. I think a lot of people don't give it more than a few minutes because the controls are so complicated, but if you take the time to learn the game you'll find a really enjoyable experience. Not perfect, but totally solid and very atmospheric. It really shows that the Jag could host games with a PC interface much better than other systems of its time due to the potential of the keypad. Sim City would've worked nicely on the Jag.
I would include Cybermorph in the underrated category too. Yeah, it hasn't aged terribly well, and there came to be tons of the dark, bland, polygonal tank games on the Jag over time. But I had a blast with Cybermorph when the Jag was new, and my friends were pretty impressed with it too. I'll never forget how great the sound quality was compared to the SNES and Genesis, but nobody talks about that today.
I've only briefly played Battlesphere at Jag-Fest a few years back, but I thought it was very highly regarded among the community. Is it worth placing on the underrated list?
On a side note, I'm surprised to see a few people mention the difficulty of Rayman. I don't think the Jag version is all that difficult. The controls are perfect and the game plays slowly enough that quick reflexes aren't too necessary. On the other hand, the Playstation and Saturn versions are made far more difficult due to the inclusion of slippery surfaces. Starting in the second area (Band Land), the slippery music staff levels make the game frustratingly tough. It seems like these were intended for the Jag version, but it was released before they could be fully implemented, and as a result the Jag version is much easier. It's one of my favorite Jag games, and I want to get into the other versions because of that, but they're just too frustratingly hard.