This question is quite old, but I wasn't really happy with the various answers. A simple way to re-indent an HTML file, given that you are running a relatively newer version of emacs (I am running 24.4.1) is to:
open the file in emacs
mark the entire file with C-x h (note: if you would like to see what is being marked, add (setq transient-mark-mode t) to your .emacs file)
execute M-x indent-region
What's nice about this method is that it does not require any plugins (Conway's suggestion), it does not require a replace regexp (nevcx's suggestion), nor does it require switching modes (jfm3's suggestion). Jay's suggestion is in the right direction — in general, executing C-M-q will indent according to a mode's rules — for example, C-M-q works, in my experience, in js-mode and in several other modes. But neither html-mode nor nxml-mode do not seem to implement C-M-q.