Hi Nirav,
If you are just looking for something that's more-or-less adequate, I've had good luck with VIM and it's internal C-indenting. (http://www.vim.org ... you have to skip past the protest splash page.)
You could set up VIM to process each of your files.
<flame bait> VIM?! Do it in emacs! </flame bait>
For formatting C/C++ files, there's also bcpp (http://freshmeat.net/projects/bcpp/). I haven't used it for a while, but I recall it was fairly good.
Cheers,
Iain
