First of all, the Jaguar is not the best console of its time. You might be better off getting a 3DO, N64, or PSX. However, if you do have this, there are some very good games for it, although the library certainly isn't as memorable as some other fifth-generation consoles. Plus the contoller is garbage... and the Disc add on should come with a guarantee that it will not work...
Probably the best game on the console. First of all, this soundtrack is pure awesome. In fact, the soundtrack was even released on its own awesome CD. You play as a ship, fixed on the edge of a colorful "web" and you shoot incoming shit and get powerups. Very addictive.
Also on PS1 and Saturn.
Alien vs. Predator
Play as an Alien rescuing the Alien queen, a predator trying to kill the Alien queen, or as a marine trying to get the fuck out. Marine campaign is by far the best, although all three of the campaigns are good. Framerate is on the sluggish side though.
A must-have for the Jaguar.
Mario Kart clone
Attack of the Mutant Penguins
A Jaguar exclusive, you play as a penguin or some cupcake thing and collect treasure, save your penguin friends etc.
Basically you control a squad of soldiers, and you have to complete the objective of a mission, divided into phases.
Whoever survives the mission gets a promotion and becomes a bit better.
Missions get pretty complex and require some creative thinking later on.
Also a definite must-have for the Jag.
Simple, yet terribly addicting.
Play as a mech in first-person view. Fuck shit up.
Iron Soldier 2
Overall improvement of the first, but same basic gameplay. Graphics are way better.
Perhaps the best port of the arcade game. Great graphics, no slowdown, perfect music.
Only annoying thing is that the score panel takes up a fucking third of the screen.
Saturn, PSX, and Jag ports are nearly identical, but this version has inferior music. Be warned that the Jag version costs significantly more than the PSX and SAT versions.
Great port, but for some reason, there's no music during gameplay.
You're in a space ship and you shoot stuff. HUD covers most of the screen, which is annoying, but great fun otherwise. Be prepared to shell out some cash for this one.
From the same dudes behind AvP.
One of the few awesome racing games on the Jag. Great sense of speed.
It's pinball. If you like pinball, you'll like this. You might want to put it on mute, though.
Pitfall: the mayan Adventure
Best version, though the 32X version is close.
Brutal Sports Football
This game is the tits, and you wouldn't know by looking at it, but this is a must own title, even for non-sports fans. Has little to do with football, and plays more like Ultimate Frisbee, giving it a feel like the cult classic "Deathrow" for Xbox. Object is to score the ball in the opponent's goal, and do so by beating the hell out of the opposing players, using punches, kicks, and 14 different powerups that appear on the field like bombs and axes. Decapitate an opposing player, and they are gone for good. Win by decpitating every opposing player or having the most points when the time runs out. Intense multiplayer makes this game hold up even today. Only thing holding back is a shitty password system and occassional frame rate problems.