You may be interested in the Minecraft Coder Pack from Ocean Labs - they include the Fernflower decompiler, producing very high quality output (certainly better than jad, tbh not sure how it compares with JD-GUI). But even better, MCP includes a comprehensive set of "mappings", providing informative names for each class, and most important field and method names.
Running a decompiler (JD-GUI or otherwise) on Minecraft by itself will produce obfuscated source, so having this deobfuscation step is very useful as a modder. If a symbol is not deobfuscated, you can submit a proposed name on IRC to MCPBot, or even provide a description for the Javadoc.
The end result of running MCP on Minecraft is a fairly readable source base, which one can easily make changes to and recompile. This is how modding frameworks such as FML and Minecraft Forge are built (although CraftBukkit uses a different approach - they don't use MCP but their own, less comprehensive and incompatible mappings, one reason why Forge mods and Bukkit plugins cannot easily be used together, a problem being solved with the merged Forge/Bukkit "MCPC+" server from MC Port Central).
Running a decompiler (JD-GUI or otherwise) on Minecraft by itself will produce obfuscated source, so having this deobfuscation step is very useful as a modder. If a symbol is not deobfuscated, you can submit a proposed name on IRC to MCPBot, or even provide a description for the Javadoc.
The end result of running MCP on Minecraft is a fairly readable source base, which one can easily make changes to and recompile. This is how modding frameworks such as FML and Minecraft Forge are built (although CraftBukkit uses a different approach - they don't use MCP but their own, less comprehensive and incompatible mappings, one reason why Forge mods and Bukkit plugins cannot easily be used together, a problem being solved with the merged Forge/Bukkit "MCPC+" server from MC Port Central).