I think it's likely it's one of the top 100 by traffic, but (not to belittle the achievements of the Stack Exchange guys) I'm sure there's at least 100 bigger sites out there by code/infrastructure.
Flight booking systems come to mind. I don't know how many web applications Microsoft would have individually (I imagine they use .NET...) and whether you want to count those (microsoft.com, bing.com, accounts.live.com, Azure...). Not to mention in-house web applications.
According to the fairly suspect Alexa they are in the top 100, world wide (regardless of technology). So by traffic I guess yes, they are in the top 100.
Clearly you can't forget it. Some teams can succeed in a wide variety of languages, some organisations can fail in any language.
Given the number of teams that have succeeded with .Net, I'd say that organisational failings are to blame for this one. Have you already forgotten the reputation of the consultants hired to implement it?
Flight booking systems come to mind. I don't know how many web applications Microsoft would have individually (I imagine they use .NET...) and whether you want to count those (microsoft.com, bing.com, accounts.live.com, Azure...). Not to mention in-house web applications.