EDIT: I read the appellate court decision and discovered some things.
First, this only got as far as a preliminary injunction, as far as I can tell. I haven't found anything about an actual trial happening. So, the legal decision was simply that Atari had a decent chance of winning at trial, and the potential harm to them justified an injunction, not that there was definitely any infringement.
The potential for infringement was based not on similar game mechanics, but rather on the more superficial similarities between the characters and aesthetics. In other words, it would be ok to make a maze-eating-chasing game that played just like Pac-Man, but featured squirrels eating nuts and being chased by dogs. It was decided that K.C. Munchkin needlessly copied some small details from Pac-man, like the ghosts and the "gobbler". This was compared to a playwrite copying specific characters and settings rather than re-telling a story in an original way. (That playwrites are not limited to 8x8 pixels and two colors when creating their characters is not touched upon in the decision.)
http://scholar.google.com/scholar_case?case=6441518363892064...
A notable quote from that case:
It seems clear that defendants based their game on plaintiff's
copyrighted game; to put it bluntly, defendants took plaintiff's
idea. However, the copyright laws do not prohibit this. Copyright
protection is available only for expression of ideas, not for ideas
themselves. Defendants used plaintiff's idea and those portions of
plaintiff's expression that were inextricably linked to that idea.
The remainder of defendants' expression is different from plaintiff's
expression. Therefore, the Court finds that defendants' "Meteors"
game is not substantially similar to and is not an infringing
copy of plaintiff's "Asteroids" game.
The Munchkin ruling also references an older case and quotes: Thus, "if the only similarity between plaintiff's and defendant's
works is that of the abstract idea, there is an absence of substantial
similarity and hence no infringement results."
It later goes on to say: Plaintiffs' audiovisual work is primarily an unprotectible game, but
unlike the bee pin, to at least a limited extent the particular
form in which it is expressed (shapes, sizes, colors, sequences,
arrangements, and sounds) provides something "new or additional
over the idea."
This was to be North American's downfall: North American not only adopted the same basic characters but also
portrayed them in a manner which made K. C. Munchkin appear
substantially similar to PAC-MAN. The K. C. Munchkin gobbler
has several blatantly similar features, including the relative
size and shape of the "body," the V-shaped "mouth," its distinctive
gobbling action (with appropriate sounds), and especially the way in
which it disappears upon being captured. An examination of the K. C.
Munchkin ghost monsters reveals even more significant visual
similarities. In size, shape, and manner of movement, they are virtually
identical to their PAC-MAN counterparts. K. C. Munchkin's monsters,
for example, exhibit the same peculiar "eye" and "leg" movement.
Both games, moreover, express the role reversal and "regeneration"
process with such great similarity that an ordinary observer
could conclude only that North American copied plaintiffs' PAC-MAN.
Had they only copied the idea the case would have gone the way of the Asteroids vs. Meteors case. Where they went wrong is that they copied the expressions used to such a degree that it was found to be infringing their copyright. Other games, such as "Rally-X" (described in Dirkschneider)
and North American's own "Take the Money and Run," illustrate
different ways in which a basic maze-chase game can be expressed.
The idea could still have been a 3D wireframe world where things try and shoot you, but it didn't have to be tanks. Atari's own Star Wars: Empire Strikes Back from 1985 shows how the idea can have a radically different expression.
There is legal precedent for outright clones being banned, and it seems to be Atari's longstanding specialty. See for example http://en.wikipedia.org/wiki/Munchkin_(video_game) from 1982. I don't know of a more current case that's gone to court though. And the real problem here is that the developer didn't even get the chance to present their arguments in court or anywhere else, Apple just decided the "case" for them.