Along the same lines....
Any prototypes worth bothering with as far as replay value?
Depends how finished they were, how much changed between development and release, and if a finished version of them actually exists.
The classic example of a game which was released but where a prototype IS still worth playing would be Trog
The prototype versions of the game were effectively a puzzle game, you placed bones at intersections to control the direction your character walked in.
The final version of Trog turned it into a simple 'Pacman' style dot eater, not by chance is the internal code of that version 'Trog 2', the development teams must have considered it a different game to the early design.
Another similar example of a similar situation would be Moon War, MAME doesn't treat these as having a parent-clone relationship due them being on completely different hardware and reprogrammed from scratch however
"Moon War (prototype on Frenzy hardware)" is actually a fun little game, with speech like Berzerk / Frenzy etc. It was programmed more as a proof of concept, maybe only one or two were produced, but luckily we managed to find all the parts of it (half way across the world from each other!)
"Moonwar", like Trog is often known as Moon War 2. It borrows a few ideas from the initial prototype, but really you probably wouldn't even know it was related without being told.
The third well known example of a game which changed massively (at least in terms of presentation) between prototype and release would be Gaelco's Maniac Square
Then there are games which were essentially finished, but failed location tests; there are a huge number of these (Atari produced a lot of them) and arguably some some of the better games in MAME fall into this category, most of these simply didn't perform well enough on location (take in enough money / gather enough player interest) rather than actually being incomplete. Some of these ended up being bootlegged, or were eventually sourced due to the prototypes not being returned to manufacturer after the location tests. There are actually probably more games in this category than MAME even has tagged because it isn't always clear if something was just very rare, or never actually released.
I mentioned Atari, so naturally you've got things like 'Beathead', 'Sparkz' etc. but companies like Gottlieb / Mylstar also had more than their fair share with Argus (Gottlieb, prototype) and Wiz Warz (prototype) The problem with most of these games is just that they were misunderstood, not really well suited to arcade play (too slow paced, too complex) or sometimes had minor bugs found during location tests which ended up causing them to miss their shipping date and were deemed too far behind the curve by the time they'd been fixed. Taito weren't immune to this, Recalhorn is one of the more interesting games on F3 hardware by virtue of being the only scrolling platform game, Riot by NMK is likely a prototype too (no official documentation lists it as released and the end credits are missing)
You've also got the infamous Tattoo Assassins which was also a failed location test / prototype, but in reality it's not actually as bad as plenty of games which were released!
The NeoGeo prototypes are also rather famous, with many of them being similar 'failed location tests' Unfortunately trying to buy many of them is near impossible, people just like waving screenshots of them around. Luckily a number of them have come to surface recently, either from bootlegs turning up, or because SNK / Playmore actually offered the *entire* library to developers for the Wii Virtual Console and the like, so rights were acquired to some of them. Ghostlop would probably be my favourite of the bunch here.
So yeah, in that sense, don't be afraid to run something just because it's tagged as a 'prototype', especially if there is no other version of it.
At the opposite end of the scale you have things "unknown fighting game 'BB' (prototype)" which really isn't much of a game at all (you see garbage most of the time, and if you're lucky get to move a character about with no actual combat moveset) It seems to be some ROMs from an early development board which was an attempt to make some kind of bootleg of Martial Champion along the same way as the Fit of Fighting bootleg on similar hardware. Things like "The Last Starfighter (prototype)" are equally unfinished tech demos (in that case we know there should be a version with at least the HUD graphics finished, but the resources we were sent didn't contain them)
Sitting somewhere in the middle you've got games which were in the middle of development, where the prototypes might satisfy an interest in seeing how the games developed "Alpha Mission II / ASO II - Last Guardian (prototype)" is one such example, it's a short (cuts off after a few levels) demonstration of how the game was developing, and if you're familiar with the final game you'll quickly notice various changes in both gameplay and art direction. Going back to Atari you've got an entire series of Agent X (Cloak and Dagger) prototypes which act as snapshots of the game being developed with new levels being added / refined over the course of them, probably not something you'd really want to play tho.
Things like 'Blaster (location test)' fit in here somewhere as well. While not a radical departure from the released game, the location test version actually has *more* waves (levels) to it, the game was refined somewhat for the actual release, but that in many senses makes the prototype a more enjoyable experience. I guess this was just a typical case of the game being tuned based on earning projections and the like.
In summary, prototype just means it (to our knowledge) didn't get an official release, it can really be anything from the first 'Hello World!' build of a game to one which probably could have, and should have shipped.
Of course prototypes aren't the only time games changed massively, even between released sets of a game the manufacturers sometimes made significant changes.
Plotting (World set 1) has a single player mode with larger graphics and no ability for P2 to join midgame when compared with the two other World sets which use the smaller less detailed tileset at all times
The two revisions of 'Tomahawk 777' are more of less different games entirely
I'm sure there are countless other examples too ;-)