I usually go with what the director wanted or intended for us to see: So with Alien, Ridley Scott was happy with the theatrical version, so that is the one I watch.
Aliens, Cameron prefers the Special edition, therefore, so do I.
Alien3, the assembly cut is probably as close to Fincher's original intention as they can make it, so I prefer that one (in this case I might prefer it anyway because it is such an improvement). I still prefer the dog over the ox bursting though.
Alien Resurrection, not sure, did he want that lame opening? The extra scenes don't really add anything. From what I remember, Jeunet said he was happy with the theatrical and I prefer it as well.