Rome: Total War is my favorite game involving siege warfare, the rest of the Total War games don't play on my computers for w/e reasons.
If any further siege warfare games are developed they have to look at cultures and eras where siege warfare actually took place, you can't really go modern with that genre. I think that's why Rome was the best of the lot, just a perfect time for that sort of game.
That said, I think I'm going to try one of the Stronghold games now, they seem to be in good standing amongst everyone here who didn't say a Total War game.