7th Voyage springs to mind, it uses Crooked Dice's Action: Engine rules mechanics. Haven't played yet, but from reading through it seems pretty good. It's definitely a more "cinematic" set of rules, though, and includes plenty of mythological elements. Of Gods and Mortals is similar in setting/tone - mortals intermingled with deities and monsters - but based on the Ganesha "Songs of..." rules, and always includes a deity in every warband (to my knowledge).
If you're looking for something with a little less fantasy flare, then there's the quite recently released "Songs of Shadows and Dust," which is also based on the Ganesha system and depicts essentially street gangs in the ancient Mediterranean. Civilians and mobs play a large role. Furthermore, there is also a planned "Songs of Shields and Spears," which I think would be more military units rather than the political intrigue of urban centers.
There is an excellent modification of GW's LOTR skirmish rules on the Yahoo LOTR Rule Variants group that includes Early Imperial Romans (and many of their allies), Celts, Dacians, and Germanic barbarians. There is also a Greek version, that has historical as well as mythological elements.
You could always use Warhammer Ancient Battles with the Warhammer Fantasy skirmish rules tacked on (may require some shoe-horning).
There are also a bunch of free rule sets, which I found here:
http://www.freewargamesrules.co.uk/ancient.htmlI think this one is supposed to be kind of popular:
http://phil-barker.pwp.blueyonder.co.uk/DBV%202003.htm