I 've only played the vanilla maps so I’m wondering what’s the best out there right now.
Top 6 Custom Maps?
My PERSONAL favourites (ie, what I like, not neccesarily the best) are:
Rhine Bridge (the new version, Rhineland Bridge is much better than the original)
Atlantic Wall
DS Bunkers
Desert Temple
Rhine is nice.
Ive heard a clan buddy talk about “a great map” where you “escort a tank thru a desert” and then “fight inside an Inca temple”. Hm, must be Temple (which I havent had the chance to see myself yet). Lol! He is a cool guy and I guess Temple is nice too!
Church has a special awesome touch to it. So well made.
// Loffy
In addition to the above I like Flughafen (haven’t yet had a chance to test the new Fliegerhorst version) and Flak Cannon. Among “oldies” I like Return to Carnage Canyon (2) 
I’ve run the following maps on my server (at one time or another):
Flughafen (now called Fliegerhorst)
Flakcannon BETA2
MML Church
Rhine2 (now called Rhine Bridge)
Return To Carnage Canyon
TrainYard
The only ones that stood the test of time were Drakir’s maps (flughafen, and rhine). I usually remove a map after a week or so if people complain about it. I’ve been running the Rhine Bridge map for over a month now. Flughafen get’s mixed reviews from players on my server, but I like it so much that I can’t take it off.