I'm starting with Youk so I can get him over with first. Kevin Youkilis is obviously beloved in Boston for tormenting the Yankees for like 8 years or so, and hitting home runs like hell. So he was a natural choice for a first pitch, though...a bit less natural than the other 2 Red Sox first pitches coming later.
Onto teams taken out in Championship Series':
As does Roy Oswalt. Another guy who's a legend there thanks to his sharp work in the 2000s, Oswalt was a perennial Cy Young finalist, a strikeout artist, and an NL Central horror figure. Even though his career was a bit less graceful than Berkman's, he still gets to come back and throw out a first pitch, which is nice.
Meanwhile, in the losing NLCS city:
...Still, I've gotta end on Yaz. Carl Yastrzemski is Boston baseball, and was more than just Ted Williams' replacement. He was legendary, and he was an extraordinary hitter. And I can only imagine the respectful applause he got when he threw out a first pitch that night, in the World Series. He deserved it, too.
I still have one or two more of these left. I imagine I'll post them eventually.