My Top 5.
Damnation- Love the verticality of the map, the skill jumps and drops, item locations that are very risk/reward, and 1v1 on it is the most tense multiplayer experience out there.
Zanzibar - 1 flag CTF on Zanzi is unforgettable no matter which side you were on. Storming in from the beach or defending the base are both where the necessity of Halo's teamwork seem most balanced and important.
Sidewinder - In my opinion, the best large map in the entire series by a mile, 8v8 CTF is the most fun I've ever had in the franchise, even if the map isn't great at many other modes.
Lockout - I've never been super interested in the MLG-style of play in the series that always gravitates towards the small symmetrical maps, but Lockout is just a perfect small arena-style map that works with just about every mode.
Waterworks - Because of the many ways you could get across the maps, the general dark atmosphere, heavy vehicles, central choke point and the secure bases -- I always felt this was the most rewarding BTB map. It could be played in so many different styles and splitting up your team into mini-squads to try stealth, warthog runs, central sniping, and defense, was always incredibly intense.
Honorable mentions: Turf, Blood Gulch, The Pit, High Ground, Burial Mounds, and Headlong.