I believe there was a site-building program that used vti directories. It's been a while, but it may have been part of the onboard site search/indexing routine. Your comment about "look mostly empty" was what struck me, that's what I remembered about them, too.
Just to take it a little deeper with Bones comment. These are used for any FP "components" or "webbots". If you do not use any of these period it is ok to delete. If you have include pages make sure to use "normal" include statements instead of the "FP include component statement". This goes for FP forms versus "normal" forms. Just investigate thoughly first is what I am trying to say. Yes I made the mistake once.
_vti directories are created by the FrontPage Server Extensions. They are used to maintain meta information about the website. They are necessary if you want to use Microsoft FrontPage or Visual InterDev to manage the site. There are FrontPage server extensions that run on most *nix web servers as well as IIS.