Hmm. Kind of difficult to think of the 5 most important protos- by not having been released originally, I can't say what kind of impact these had. I'm kind of concentrating on what I feel actually affected the collectors; protos began leaking in the early 90s, and a lot of the fights, questions, and controversies that are around now were first prefigured by the 5 I list below.
(I also hesitate to include protos that haven't been discovered; as much as I wish SQ: Airworld were around, but since there hasn't been any sort of find, it has had zero impact. Perhaps there should be a separate poll of what the 5 most wished-for protos would be?

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In no particular order:
1) The BEST prototypes: There are a slew of various titles, and some are thought to be reproductions, but the BEST protos that were being sold in the mid 90s were the first chances players got to try things like Holey Moley, Sinistar, Klax, etc. If it hadn't been for BEST, these things would have gotten out in a more piece-meal fashion (or simply tossed out), with less of an organized effort by collectors to snap them up. People hated the commercialism, but it was commercialism that got these into our hands.
2) Tempest: This was out-of-left-field when it surfaced; everyone figured a 5200 proto was around because of the catalog announcements, but when a couple of copies of this surfaced in the mid-90s, it was a surprise. And, like usual, it took years for a dump to be made and then released. I believe that the first inkling that this existed was when a magazine did an article about the inner-workings of mid-90s Atari, and a lot of weird stuff came tumbling out; 2600 Tempest, Bionic Breakthrough and the Mind-Link controller, Rabbit Transit on cart.
3) Star Wars: Ewok Adventure: There were a lot of bad feelings about this one for years; the owner of the only known proto wouldn't let a ROM be released. Though that problem has plagued other protos, SW:EB was a *very* high-profile title thanks to Parker Bros. catalogs and Star Wars fandom. Discovered in 1997, the same year as Save Mary and Good Luck Charlie Brown. (My personal fave from 1997 would be GLCB, just cos I'm a Peanuts fan.)
4) Alligator People/Planet of the Apes: The ROM release of Planet of the Apes in 2000 was another long-sought game... too bad everyone thought it was Alligator People. This was a proto that took nearly 5 years to release; again, the owner wouldn't let it get dumped or released. The true Alligator People ROM, however, was kind of anticlimactic. (As an aside, Tempest, I note that the original owner of Planet of the Apes in 1995 thought it was Alligator People only by guess-work, not because of a mislabelled cart casing as noted on your site. See this
archived poston Google to see the logic that led to the game being called Alligator People. Here's a separate
post by a reliable early RGVC'er who apparently compounded this misnaming error by "confirming" that it looked like an Alligator People-esque game; his post set off a heated argument about the morality of hoarding protos. If nothing else, the background story of this "original AP" and incredibly angry feelings engendered would make for a good write-up on your site.)
5) Atari Kids prototypes: Separately, these games might not have caused players to salivate back in the day, but the sheer number of unreleased kid-friendly Atari titles from the mid-80s left a lot of question marks on 2600 release lists. The eventual discovery of Donald Duck's Speedboat, Snow White, Garfield, Good Luck Charlie Brown, Grover's Music Machine, Asterix/Obelix, Peek-a-Boo, Dumbo's Flying Circus, Miss Piggy's Wedding answered a lot of questions.
Honorable mentions: Combat II (another mystery from old Atari catalogs solved), Polo (another out-of-thin-air game), Elk Attack (kindly released by its original programmer, and a pleasant surprise; no one knew it had existed), the Amiga protos (sold through a now defunct mail-order company, its mention in an old Game Doctor column was the first time I discovered the world of 2600 protos), Pink Panther, the licensed Mattel protos.