I asked Xilinx for such a list but they don't have a complete list. I wish to make sure all input files are in source control and all output files aren't. This is with 13.1-13.2 with ISE and PlanAhead
Some of the information they have provide is the list of PAR Output Files and the ISE Design Suite Files in the Command Line Tools User Guide, the source files list from here.
Edit Aug 19 2011: mentioned 13.2 and PlanAhead
Edit Sep 7 2011: removed EDK reference since some in answer
Best Answer
Quick answer: No such list exists, anywhere.
Long answer: I could tell you, but then I'd be wrong. I've been using Xilinx tools for the past 15+ years and every time they come out with a new version (or even a new service pack) things change. Sometimes even just changing various XST/MAP/PAR options will cause new files to be generated. So even if I did give you a list it would likely be out of date or just wrong.
I've created my own makefiles for building my FPGA's (I'm not using ISE's GUI environment), and it's fairly well documented what the input files to the various tools are (XST, MAP, etc). Everything else is not required and thus doesn't need to be checked into the source control system. My makefiles have a "make clean" option that removes all of the extra files. So when Xilinx releases a new version I simply recompile and the "make clean". Any file that remains (and isn't obviously something I need) is considered to be junk, and I add those files to the "make clean" list of things to delete.