Edited your title to include "spoilers" (even though I imagine everyone here has played the campaign).
Yeah, I've wondered the same. I very much doubt they were with Shepherd - they were TF141 and Shepherd went out of his way to kill them all. Remember the car that picked up Soap and Price? That was being driven by a TF141 guy. He got shot, presumably he's dead, but I don't think Shepherd could have gotten all of them. They were meant to be the best of the best and once they realised what was happening (and they should have realised it very fast if they were the 'best'), then they would have melted away.
As for Archer, he was a fair way away from the house to start with while he was providing sniper support and he wasn't running with you when you're making your way to Shepherd at the end there. Furthermore, after Shepherd kills Roach and Ghost, he makes tells his men to take off. So presumably they get straight back in the helicopters and bugger off, leaving Archer very much alive.
I can't remember Toad though - was he a sniper in that mission as well?