I think I'd go first and foremost with the LOTR variants from the Yahoo group if you want Romans vs. Barbarians, or even just the LOTR rules, using "counts-as" profiles in place of the various fantasy minis. You could easily count Romans as the more heavily armored and disciplined Gondorians, orcs could represent a variety of barbarians (their profiles range from relatively weak, with poor morale, to quite strong and heavily armored).
Song of Shadows and Dust would be good if you're interested in an urban setting, and/or if you want a game with campaign progression, though. Additionally, if you're interested in later Romans, there's always Song of Arthur and Merlin, which is the same core rules but covers 3 versions of King Arthur (historical, Welsh folklore, and high fantasy). Obviously you'd be looking for the historical version, but if Arthurian wargaming in general appeals to you, then this is one of my favorites for capturing the feel of that type of small-scale heroic combat.
I suppose it's also worth looking
here, since there are tons of rule sets listed (not all skirmish, though). If you like DBA, there's a set in there by Phil Barker called "De Bellis Vellitum."
Another option would be to use WAB along with the fantasy Warhammer Skirmish supplement, applying the skirmish rules to the historical game.