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I was at DDD9 on Saturday (Community MS conference) and there were a lot of startup folks there. I think it's too easy to get caught up with a subset of the community (say the mobile startup community or the rails community) and lose sight of the bigger picture.

Certainly among b2b startups BizSpark has encouraged a lot of startups to go with the MS stack where they previously would have gone with Rails, etc. While consumer startups seem in general to be more often based on non-MS stack there's plenty of MS stack consumer startups (PlentyOfFish, Just-Eat, StackOverflow) which have become the dominant players in their field.

When it comes down to it, for most startups it doesn't really matter what your stack is, just pick the stack that you're most productive with.