its not really a good idea to go chmod -R'ing, and to be honest not worth it, for the amount of time it takes to su, cp/ln, exit. and some files need to be owned by root so copying them there as a different user wont work. and dont forget the security risks involved, ask yourself why linux viruses are almost non-exidtent. chown would probably be a better(not much though) option than chmod. but anyway
dont go chmod -R'ing anything with a bin/sbin directory in it. dont add executable permissions to non executable files - this has the possibility of making autocomplete an absolute nightmare. avoid /var, /home, /tmp, /etc, /dev. apart from that you should be ok - dont quote me on that i could have easily forgotten something.
if there are readonly areas you write to regularly, then consider putting the actual files somewhere else and symlink the directory to where it should be, thats a much neater solution