A. There's a number of levels of association of similar questions
$\quad $ (4 by my reckoning, if we also count 'not quite similar enough to do anything'):
Where the questions are exact duplicates, to the extent that they invite identical answers - and both have answers - they should usually be merged (preferably into the better question; if they're of similar quality, merge into the older one). If they don't both have answers, treat as 2.
Where the questions are asking the same thing - to the extent that answers to one will solve the other question, but the answers themselves don't really answer the other question, one should close as duplicate; again the better/more canonical question should normally survive, though the quality of answers and age are other factors to consider.
Where the questions come close to asking the same thing, but in a different way -- in a way that invites questions that to some extent explore different aspects of the issue -- then they should probably both stay open, but be linked (both ways) via comments. See this earlier post for some discussion of that issue (see the Jeff Atwood quote in particular)
B. I suggest doing it in stages
I suggest taking care of flagging any you think should merge first.
Then depending on your privileges, either vote to close as duplicate or flag the ones that should close as duplicate.
Then link (via a comment in each) any that should still stand separately but where the answers to the other question may still be useful.
[I'd also suggest that with wholesale flagging, to avoid overwhelming the flag queue -- about half a dozen flags at a time is no problem, but two dozen in a day on the same thing (some people can do that many) might lead to missing a more urgent flag (such as a spam flag). If it's a lot, spread it out a bit. This also has the advantage that if posts do get bumped, the front page isn't full of old questions all on one topic.]