People are acting as if Wesley Wolfe (Wolvereness) is trying to claim ownership of Minecraft server code. I don't know him, but that is not his intent from what I've seen. It is simply to have his code removed from a project with a clear conflict of interest over licensing. From what I have seen, it has been a case of: 'remove my code from the project OR opensource the Minecraft server code'.
The fact that this brings to light that Bukkit is no longer eligible to use its codebase because it's in violation of its own license is just a bonus.
Unfortunately Spigot is suffering from a side-effect of this claim. It was built off the Bukkit source code, so if Wolvereness were to leave his code in that project, without a DMCA claim, it would dilute his legal position against Mojang.
Here are the facts as I see them:
1. Bukkit is an open source project, licensed under the GPL.
2. Many developers, including Wolfe, contribute code to the project under the GPL terms. The developers retain copyright over their contributions.
3. The Minecraft server was reverse engineered (apparently in violation of Minecraft's EULA) and the resulting decompiled/de-obfuscated code initially included in the CraftBukkit project.
4. Projects like Bukkit, Forge and Spigot add considerable value to Minecraft, but are not (initially) controlled by Mojang.
5. Mojang surreptitiously acquires the Bukkit project by hiring a number of the project's key developers. While the hiring of the developers is made public, the acquisition of the project is not.
6. The developers Mojang hire work on Bukkit-Minecraft "intergration". Bukkit features get added to Minecraft's server, and proprietary Minecraft server code gets incorporated into Bukkit/CraftBukkit.
7. Community developers continue to contribute to Bukkit, under the GPL, thinking they are working for an independent project.
8. Bukkit/CraftBukkit is distributed during this time, under the (L)GPL, including the proprietary code. This is a violation of the (L)GPL.
9. Mojang changes EULA to prevent 'pay to win' servers, and asserts Bukkit is subject to that EULA too.
10. The majority of developers vote to discontinue the project. Mojang steps in publicly to say that they can't do that and they have owned the project for two years.
11. Mojang asserts control over the entire project, including contributions from community.
12. Wolvereness DMCAs the project, for the removal of his code.
13. Mojang claim they added no code to the project, yet the project had been distributed for two years including Minecraft server code while the project was supposedly in Mojang's ownership. Mojang have been aware of licensing issues since 2011, but have done nothing to remove their proprietary code from a GPLed project in the time since they acquired it. Licensing of the project has not changed.
It seems that there are only four possibilities: Mojang kills Bukkit and walks away; Mojang rewrites Bukkit to remove/rewrite code from outside contributors and closes source; Mojang caves and opensources Minecraft server code; Mojang takes Wolfe to court to determine outcome (which could take years of appeals).