Popping back in with two more additions. The first is Unbridled Fury which aims to be a generic wargame suitable for any setting but started out as a fantasy game and mainly emphasizes settings based in that. Also, don't be fooled by the fact it's 178 pages as there isn't much text on each page and the creator and community appear to have been inactive for a while now. Another is Fury of Elizium, which can be run as a skirmish game but mainly emphasizes larger scale battles.
EDIT: I think Quick Intermediate Level Skirmish is also worth mentioning as, while the core rules are generic and only 8 pages long, there are a great amount of supplements for it, some of the fantasy genre, that greatly expand upon them.