Google Transit does Seattle
They started in Portland about a year ago, but now Google Transit has a site for Seattle.
For example, it says that for me to get from home to my office right now (at 6:30 on a Saturday morning) would take 58 minutes. That is, 58 minutes after my bus arrives near home, which won't be till 8:52am.
It seems to be hooked into the same GPS systems used by other sites, but the UI is the best I've seen yet.