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.
High priority items are:
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More input plugins. Currently there are plugins for XMMS and Winamp; Freeamp is in the works. More is better!
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Improving the compression methods.
Some other "nice-to-haves":
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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...
Things that are in the works (check the flac-dev mailing list):
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Windows ACM codec.
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FLAC module for Audiofile.