Wow, what a list! Seriously, I didn't realize until seeing them all laid out like that how strong the two-parters actually are. Virtually every choice is a candidate. I went with "What's my Line", but it was incredibly tough. I chose it not because it's the "best" set of the series (I think "Becoming" gets the nod there) but because those were the episodes where BTVS really picked up for me. I had enjoyed S1 and liked much of S2 up until that point, but those were the episodes that made me really sit back and just go "wow". I loved the Buffy/Angel stuff (which I always do), Spike was amazing, the Order of Taraka was an interesting concept and it had some great character moments for Buffy.
But man, now that I think about it, not choosing "Becoming" or "Surprise/Innocence" was damn tough...