That reminds me; not only does Halo 2 have the best soundtrack, but it also uses its soundtrack the most effectively during gameplay.
Halo CE is not short of good tracks. The problem is that music tracks are often sparsely spaced apart, especially in longer missions like AotCR where stuff like Rock Anthem to Save the Universe would play and then stop. It is an awesome track, but everytime I play that mission it feels out of place since IIRC it plays during one of those random and barely distinguishable rooms.
I feel that Halo 3 is somewhat similar with good tracks playing over inappropriate times, or were simply out of place for what was happening on screen. I'm not saying that this is always the case, but a few examples like this contribute to the overall impression. There are a number of examples that suggest otherwise in both games (Covenant Dance in CE, the two Scarabs battle etc).
Halo 2 is completely different. Playing through missions like Gravemind and High Charity with the perfect suites to go with them, in beautiful environments while the Covenant is tearing itself apart... I don't think moments like that can be topped outside of a cutscene.
Other examples include Peril in Delta Halo, etc. Even some of the (arguably) more disliked tracks, like those from Incubus, actually suited the combat well. I vividly remember the Banshee fight in the Arbiter with that guitar music in the background.
You can have good soundtracks but the best Halo missions use them in the most effective way to build up an atmosphere. Halo 2, while imperfect, is simply the master of that strategy, IMO.
This is also why I don't judge soundtrack samples too harshly until I see them in action. I still don't like parts of the new Gungrir Mix, but it just feels better when it plays in the background of Halo 2 related action.