GeoNames (http://www.geonames.org/) offers a downloadable database of cities with more than 15k population and their time zones. They list aliases as well. That's what Zeitzono uses. Just use that.

(You don't have to use all the listed cities if it slows down the hTime web app, just pick some minimum population threshhold (eg. every city larger than 100k people) and use those.)