FLAC is an open source project and we are happy to enlist the help of anyone who wants to contribute. You can do this to a limited extent through the mailing list but if you have major changes to make to the code it's best to sign up as a developer. In either case, make sure to check out the FLAC goals first; there are some thing the we don't want added to FLAC, like copy protection and lossy compression.
There are several areas that are especially important:
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Testing. Since FLAC is still beta this is number 1. If you are a lossless encoder you have to be absolutely lossless for all input. The test suite has patterns that are designed to strain the encoder to the limit but more test cases would definitely help.
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More input plugins. Currently there are plugins for XMMS and Winamp; Freeamp is in the works. More is better!
Some other "nice-to-haves":
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Improving the compression methods.
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Fix the MSVC makefiles to make libFLAC.dll (instead of just the .lib).
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Configurable ID3V1 support and ID3V2 support in the plugins.
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Support more input types than just WAVE and raw in flac.
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A better logo! Gimp jedi I'm not...