.., tower, tomb, temple, ...
Basically a "site" as defined in game is any point of interest on a map. In the current release, player made fortresses and human structures are the only sites that have any architecture to speak of (excluding roads and bridges, but those are map features, not sites). The sites of the other races are represented on the map, but if you visit them, there is nothing there. It's as though you walk to the place on the map where the world map says "Dwarf MountainHome Here" but you're just standing on an imaginary "X marks the spot" with not buildings, items, anything.
What will be happening in the next release is that more of these points of interest on the map will be fleshed out in a more meaningful way. As far as we know, Kobold sites still won't be re-introduced.
A number of site types had been available to visit with buildings, etc. in previous releases of DF. However, Toady wasn't happy with how they worked in the world, and removed them until he could make them work better. That time is now. Moving forward, a site will be a location, or area that an entitity (creature, band, civilization, cult, etc.) has, or has had, some degree of claim to.
Something I will be eagerly looking forward to is how World Activity (I can hardly call it World Gen anymore) will deal with necessarily culling sites. What of the site that a small cult had claim to for only 2 years, in the middle of a desert, and had only begun work on their first wooden shrine, barely 5 tiles of work? Will this persist for 500 more years? Will the site claim diminish, only to vanish in 10 years? 20 years? Without an entity occupying the site, will the walls crumble to dust? When there is no recognizable architecture or artifact (in archaeological terms) readily recognizable, will the site simply fade back into the surrounding biome? Or will there be persistent, but ever harder to discern sites persistent ad infinitum? Would you be able to harrow a feild, one day in the future, and turn up a coin from a once powerful city state? This find sparking excavation of the remains of the site that stood in this spot in the Age of Myth?