There's an awful lot of guesswork and name-calling going on here, and a sense that the argument is divided into "Mojang sux!" and "Mojang rulez!" camps. The truth is of course, way more complex. Here's an attempt to lay out some (hopefully) objective facts, mixed with my subjective opinion. Disclaimer: I've been involved with Bukkit for over 3 years as a plugin developer and contributor to the forums, and (very minor) contributor to the Bukkit project itself.
* The Bukkit project was started late 2010/beginning 2011 as a replacement for hMod, an earlier server mod, by 4 people: Dinnerbone, EvilSeph, Tahg and Grum.
* The Bukkit project consists of two main deliverables: the Bukkit API, licensed under the GPL, and the CraftBukkit server, licensed under the LGPL.
* The Bukkit API contains no Mojang code. It's the Java JAR against which Bukkit plugins are compiled.
* The CraftBukkit server contains a copy of the Bukkit API (via Maven shading), some original Java classes in the org.bukkit.craftbukkit Java package (most of which either implement Bukkit API interfaces or serve as glue code between Bukkit and Mojang's own code), and decompiled/semi-deobfuscated copies of Mojang classes from Mojang's official minecraft_server.jar.
* Effectively craftbukkit.jar contains code with three separate licenses: GPL, LGPL, and Mojang's proprietary license. My opinion: "what the hell were the Bukkit team thinking when they chose this license model?"
* Mojang were presumably aware of CraftBukkit from the start, it being the pre-eminent server modding platform, but chose not to take any legal action over the inclusion of (decompiled copies of) their code in a GPL'd project. In fact, Mojang even went so far as to supply deobfuscation mappings to the original Bukkit team, so it's very clear that they supported the Bukkit project. My opinion: "of course they would, it's helped their sales enormously"
* Early 2012, Mojang announced that the original Bukkit team (Dinnerbone, EvilSeph, Tahg and Grum) were being hired to work on Mojang's own planned modding API. Note that this API had been announced some time before, and has yet to materialise.
* Apparently at the same time, Mojang also acquired rights to the entire Bukkit project. This, however, was not publicised.
* The Bukkit project continued under new direct leadership (mainly feildmaster, Wolvereness and Amaranth) after the original team were hired by Mojang. feildmaster recently stated that Mojang stopped providing deobfuscation mappings shortly after the original team were hired. However, Mojang allowed the project to continue, and did not take any legal action over the CraftBukkit server.
* EvilSeph left Mojang shortly after, and is the only member of the original four to remain involved with the Bukkit project.
* Cut to last month: EvilSeph posted an announcement that the Bukkit project was being ended, due to the increasing difficulty of updating it for new Minecraft releases (remember: no more deobfuscation mappings from Mojang), and concerns of its legal status being exacerbated by Mojang's recent EULA changes.
* At this point, Mojang sprang into action, asserting ownership over the entire Bukkit project. Dinnerbone tweeted that he'd personally update Bukkit for the new Minecraft 1.8 release. Mojang's Jeb confirmed that Mojang owns Bukkit (I quote his tweet: "we checked the receipts"), having acquired it when the original four joined Mojang in 2012.
* The revelation over Mojang's ownership of Bukkit caused very significant consternation for many contributors to the project (there are around 170 individuals, including myself, who have contributed code licensed under the GPL).
* Wesley Wolfe aka Wolvereness, one of the new Bukkit dev team leaders, filed a DMCA takedown notice on Sep 5th, on the grounds that Mojang cannot legally distribute CraftBukkit when it contains both GPL'd code from him, and proprietary code from Mojang.
* In the last couple of days, pretty much all of the existing Bukkit staff (forum administration, plugin review & approval...) have resigned, effectively gutting the project.
* Also in the last couple of days, a new modding initiative called Sponge has been started by many individuals from the Bukkit project as well Forge, Spout, Flow - other leading Minecraft modding efforts. It's intended to be a higher-level abstraction layer on top of Forge, and won't be Bukkit compatible or contain any code from Bukkit. Given the calibre of many involved and the solid foundation of Forge, it has a very strong chance of success IMHO.
So those are the facts, basically. My opinions:
* The Bukkit team should not originally have chosen a LGPL license for CraftBukkit. And given that the Bukkit API is licensed under the GPL, and distributed in the CraftBukkit JAR file, this was also a poor licensing choice.
* Mojang had the opportunity to complain about this licensing decision at the start. Not only did they choose not to, but they provided tacit support to the Bukkit team, and later hired them as developers for their own API.
* Mojang's failure to make it clear that they owned the project subsequent to hiring the original dev team was unfortunate, and left many contributors feeling deceived when their ownership came to light. There is a feeling that people were being tricked into writing code for Mojang for free, when they believed they were contributing to a community-driven project.
* Wolvereness's decision to file a takedown is justified, although it's stirred up a huge amount of resentment from people who believe they're automatically entitled to software that he and others have spent a lot of time writing for little or no recompense. In addition, it may have the useful effect of forcing a solid resolution to the affair.
tl;dr Bukkit is most likely dead.