Our DMS Software Reengineering Toolkit has been used on huge C systems, parsing, analyzing, transforming, and regenerating C code. Runs on Windows, and will run on Linux under Wine, but it does handle Linux-style (GCC) C code.
I can't emphasize enough the ability to round-trip the C source code: parse, build trees, transform, regenerate compilable C code with the comments and either prettyprinted or with the original programmer's indentation. Few of the other answers here suggest systems that can do that robustly.
The fact that DMS is designed to carry out program transformations (as opposed to other systems suggested in answers here) is also a great advantage. DMS provide tree-pattern matches and rewrites; it augments this with full control and data flow analyis to be used to extend the conditions that you'd like to match. A tool intending to be a compiler is just that, and you'll have a very hard time persuading it not to be a compiler, and an instead to be a transformation engine as the OP requested.
See https://stackoverflow.com/a/2173477/120163 for example ASTs produced by DMS.