For me it would be:
1. "What You Leave Behind" - The most natural conclusion, with the crew parting and moving onto other things at the end of the war, with each of them getting their own little farewell montage.
2. "All Good Things" - Despite the time-travel / dream plot I liked how it harked back to "Encounter at Farpoint".
3. "Endgame" - This is where things get difficult. Not a huge fan of this finale as by this time I wasn't watching VOY (but seeing what's left it is the only option for third place). By the time it aired time-travel was beyond tired, the super-ship was pointless, the Borg were further de-clawed, and after they get back to Sol we get no conclusion for the characters. Neelix was only in one scene (too many) though.
4. "Turnabout Intruder" - Honestly I can't remember the last time I saw this episode, but even TOS at its worst was better than ENT's finale.
5. "These Are The Voyages" - Awful. The craming in of the TNG plot element was pointless, the needless killing off or Trip was just infuriating, jumping forward six years made no sense (especially when no one has been promoted). Anytime I think of ENT, I blank this episode from memory--it brought down a decent season.