Of the most popular cores (Trinity, MaNGOS and Skyfire), they've all continued on from v3.5.5a. MaNGOS (Now I guess known as CMaNGOS) was working on a v5.x core but as far as I know a fight happened and they stopped development and are mainly on v4.3.4. Trinity also was working on a v5.x core with SkyFire but Trinity went on with their own which now seems to have vanished and SkyFire is privately working on a v5.x core, I'm not sure when they're going live though. But they all still have cores in previous versions as well.
As of Cata, Blizzard made it significantly more difficult to get opcodes since they change on every update so once Blizz releases an update, devs can't sniff for opcodes anymore and there are a lot of them.