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I see Hipmunk still doesn't track budget airlines in Europe (eg, EasyJet).

Which makes it fairly useless to me, and absolutely not a replacement for Kayak.

Hipmunk does have EasyJet, in fact.

Do any flight search tools track budget airlines?

Adioso was adding a lot of budget airlines up until recently. It's worth checking out.

Another site for budget airlines is travelfusion.com They also have an API

skyscanner.net does (or has done in the past anyway!)

Still does. They've got almost every European budget airline, actually. And I hear they have pretty good coverage of the Asian market, too.