Different cores = Different coding style and sometimes different programming language altogether.
None necessarily better than others. However, Arcemu is essentially the younger brother of Ascent (Which is the yet younger brother of the old Antrix core), which is now basically dead aside from the very few people that develop it in their free time. Arcemu used to be good however it's not really any good anymore.
Of the sections on Ragezone, MaNGOS is the best. It's derived from a leaked version of Wowd, which later became Ascent. However, even though it's beginnings were derived from Wowd, it's almost completely different now. It's still developed fairly frequently and if I remember correctly either they are working on a 4.x core or said they will never. MaNGOS also supports v1.12.1 via MaNGOS Zero and v2.4.3 via MaNGOS One. The current most version supported by MaNGOS is v3.5.5a.
But for a v3.3.5a core I highly suggest Trinity core, it seems to be much more developed than MaNGOS.
There are also MANY other cores, some still alive, many dead and many proprietary. As far a v4.x cores go, as far as I know there is only CactusEMU (Died about a year ago), Arkania, Trinity (Still early in dev I believe) and SkyFire, whom is the best. Trinity is working on I think v4.2.0. Arkania is on v4.0.6a (However, rumor has it they copy/pasted most of their code from SkyFire) and SkyFire has a mostly developed v4.0.6a core and are working on a v4.3.0 core.
