Instead of cscope/ctages, have you tried GNU GLOBAL? I've taken my first steps with it and the ggtags mode. So far, I am finding it to be drastically better than ctags.
I didn't even know about it. This looks awesome. Highly recommend: wrap GNU GLOBAL in a web app (scrape its output, stick it in a database). We did that at Matasano (with dumber tools than GLOBAL) and not only was it incredibly useful, but shockingly, shockingly easy.
I didn't know GLOBAL had a web interface, but we generally want search, highlight, bookmarks, and notes, in addition to clickable cross-reference popups. We used ectags and Pygments.
Makes sense, I think. As I said earlier, I am new to GLOBAL entirely. Something I found as I was building up my new emacs setup at work. So far, I've been impressed. Not sure I'll ever care for the web interface, but the ggtags mode has been a dream. And I've really only used find-references and find-definition.
Have I just never configured ctags correctly?