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.