I think stamina is the best way to prevent jumping, like in BF2. If you jump, your accuracy goes down and you run out of stamina and um, can't run away.

Halo 2 did jumping rather well, I think you slowed down in the air and had little airborne control. If you jumped, that just made you a slower target, but you had to jump to avoid grenades sometimes... You couldn't really bunny-hop effectively in that game.

If this is a conversation about game design, then I'd say that Jumping could be removed, but only if it is also replaced with some kind of dashing action. For a FPS, this probably wouldn't make absolute sense in terms of animation, but is an important tactic. Someone mentioned before that jumping was a way to get away from rocket damage. This happens because jumping increases your overall speed (not on the floor's X or Y axis, but in the air's Z axis) and got you away from the center of the explosion faster. Losing the ability to jump would give too much power to any kind of splash damage effect, and remove ability from the defender, laying only accuracy on the attacker as the gameplay factor. Because these are multiplayer games, and we want each player to have a chance to really play, the defender needs a way to get away from that attack, and some kind of dash would assist. Of course, we don't want them just dashing all over the place, so the dash would need some kind of slow down toward the end of it, so that it's no faster than normal running, but still a better way to get away from an explosion than plain running.

If you want to see Jumping Done Right™ in an action game, look at Unreal Tournament 2004. Watch a demo of a guru battle and you'll see tons of jumping, but if you pay attention you'll notice that nobody is bunny hopping around - every jump has a purpose, and jumping at the wrong time is deadly. No stamina needed.

For semi-psuedo-realistic games, a stamina bar is better than the "jump-stumble" that made it in Counter Strike, but honestly who cares? Just make the cone-of-fire large while jumping (and triply large if firing fully auto while in the air) and it shouldn't be a problem.