For me it's never not been Monkey Island 2. The only thing that has fluctuated in my mind is how thin the margin is.
The original is an undisputed classic, the game that showed off the true potential of a SCUMM adventure game and more or less represents the best of a genre and the halcyon days of LucasArts as a spirit. I don't think the series ever really did fully recapture that kind of Princess Bride storybook flavor it had going here. I can't imagine arguing with anybody who would rank it first, though I find it hard to find any new way to sing its praises at this point.
Monkey 2 feels like it builds on the first game and offers a deeper, richer, more ambitious experience. It ups the ante in every way, and to this day you can pit the Four Map Pieces segment against pretty much anything the genre has produced since. Again, three decades worth of discussion sort of leaves me at a loss to come up with some kind of original take on the thing, but for me this is still my favorite game.
CMI is an undeniable departure from the first two in overall feeling for reasons both unavoidable (major technology gap, different creative personell) and chosen, and it probably honors the template of the original a little too much in the first half (get ship and crew, insult sword fighting) but it's just such a well-made adventure game top to bottom, with stupid good production values, that I doubt a convincing, objective argument could be made for it representing any kind of misstep from a strict quality standpoint. It's another installment where I can't object to it being ranked first. It is also as influential as the first game in a certain sense as it seems to have spawned, or at least been released at the right time to soak up, that initial burst of online fandom. Many people seem to have met the series through CMI.
EMI is the least of the games, but I think it deserves reappraisal in terms of what that really means. What I see is a satisfying, rock solid adventure game with a lot of funny moments, good animation and very possibly the best voice acting in an LEC game -- and that's really saying something. On the other hand it delivers a somewhat off brand story for a Monkey Island installment, it comes dangerously close to making the world feel too small (that Tri-Island Area map: hilarious) and it unquestionably fails its pedigree on the graphics front (both because using GrimE to create a cartoony-yet-lush 3D world with the target specs of the average turn-of-the-century Windows user isn't setting yourself up for success, and because Chris Miles, by all accounts a talented animator, probably wasn't the guy to sit in the Art Director chair for the series' delicate transition to 3D.) But visuals aside I think it's held up reasonably well, and I would like to think its status as a kind of "side trip" story will gain some appreciation/perspecitve now that it is a middle installment and not the last game, which admittedly was not a good look for it. Monkey Island is an exceptionally good series, and in this case being the worst of five great games still leaves you: a really good game.
TMI is a bit of a rebound that to a large extent feels like a course correction or return to form, especially in terms of a moody atmosphere and a general sense of captivating piratey-ness (both of which were a bit lacking in EMI as a consequence of its story), and the Telltale engine really upped the ante on the "performances" in my opinion, allowing the installment to go into some new emotional territory. On the downside, the decision to develop the episode with WiiWare in mind and general corner-cutting absolutely and unnecessarily hurt the production values. The art direction is good, but the 3D is up against limitations it should not be up against, and it is kind of funny how the Xerox-character-designs-for-background-NPCs strategy never really improved on Monkey 1. And while the MIDI score has a certain nostalgic feel that I like, it is kind of shameful that Michael Land's excellent compositions were not given the respect of a proper production, which might well have resulted in something that could have usurped the CMI score. The game's qualities more than overwhelm these drawbacks, it's just frustrating that they feel so self-inflicted. On the quibbles front, the equal-sized chapters necessitated by the episodic structure made me weirdly sad, I object to the absence of Alt+W, and the abruptness of the last moment felt like the one real shortcoming of CMI wasn't learned from.
Short version: All these games are great, and I question the value of rankings, but I give the crown to MI2 if coronating one is a life or death matter. And I look forward to buying them all yet again in what promises to be a truly absurd anthology package in October.