Whatever you guys do when visiting here, Don't Stay At Any Place On Aurora Ave! You'd most likely catch things worse than bedbugs.
For a good central location in downtown, the Ace Hotel gets accolades. The Days Inn on 7th near Denny is a neutral choice. A friend of mine usually stays at the Moore, which apparently is the cheapest, but I don't know the hitches with that deal.
The most central spot for drivers who want to stay outside downtown is the Silver Cloud on Broadway & Madison in Capitol Hill. Not the cheapest, but I've heard unanimous praise for that location. With every place, you can find cheaper, outlying places if you drive.