Oooh. Good questions Lara. I have seen season 4 but only once when it originally aired.
There is a whole part with him on New Krypton ship. But the very very first time he comes back, I seem to remember him being in civilian clothes (oh and there's also a dream where Lois think's he comes back - again he's in civilian clothes). Anyway, he comes back for a "visit" to Lois in civilian clothes. She ends up and goes back to the ship as a concubine with Ching to surprise Clark.
I think the first actual time you see him in a *suit* after he comes back - he is back in his red and blue suit.
And as far as what he comes back in... they never really show that I don't think. But I could be wrong - it was a long long time ago. I'm thinking that he probably used some kind of shuttle between the ship and Earth, but that's just a guess.
So anyway there's my opinion and the little info I remember.
