Many seemingly confused and/or contradictory summaries here...
Here is my attempt:
1. Company (Mojang) releases game (Minecraft) + multiplayer server under closed license
2. Third party uses decompilation to create derivative work of server. Creates GPL project (CraftBukkit) in violation of both Mojang's license and the GPL (all code must be GPL). Mojang does *not* try to stop the unlawful redistribution.
3. An individual (Wolfe) contributes GPL code to this project.
4. Mojang hires devs of CraftBukkit and thus gets 'some kind of control' over CraftBukkit.
5. Wolfe submits DCMA takedown to those who redistribute CraftBukkit becasue it is in violation of his code's GPL, since it is distributed integrated with non-GPL code.
Note that *redistribution* is the key for the GPL license. The important question is thus: did Mojang ever *redistribute* CraftBukkit themselves? If they did, at that time they released the *decompilated* server code at whatever license it was specified. But, if there is nothing resembling an official Mojang release of a Bukkit binary or code, then nothing of this matters for them. The only people who then are in the wrong are the ones who redistributed a combination of a GPL and Mojangs closed source. They are liable both to Mojang (who are not currently complaining) AND the people who's GPLd code are used (one individual who now IS complaining). Per the DMCA takedowns they have to stop this redistribution.
Furthermore, IF Mojang did distribute this binary or code themselves, it appears some people (possibly Wolfe?) argues that this requires them to also open the original source code of the game server. That is an actually very interesting non-obvious license discussion. Personally, I don't *think* it has legal standing. The fact that Bukkit was built on top of the decompiled code makes Bukkit more of a normal derivative work from the decompiled code than the original minecraft server code. It would be a widely different matter if someone contributed obfuscated code to an already existing GPL project and then redistributed the combination.