I've started working with an SEO on a few things and I've seen a few things he does. mod_rewrite hackery is a part of it, as is validated HTML,/CSS meaningful titles, reducing load times as much as possible (basically doing well in all Yslow tests), accessibility stuff and other bits & pieces (like generating XML sitemaps, product feeds for Google product search etc etc).

A lot of this should be covered by any half decent site but as you may not find surprising, most sites out there don't know or don't bother.