Adioso is great - I love the date/price graph you get across the top of each search. It was super helpful in finding flights for my holiday to the US (PER-LAX) in August, which I booked just last week. I know very little about startups, or even how this article relates to your current situation, but I hope you guys do well.

edit: Some features I would love:

-'I need baggage' and 'I'm paying with a credit card' checkboxes which would add the relevant fees to the fares. From an Australian standpoint, sometimes the difference between a Tiger fare and a Virgin one is far less significant once you add fees.

-A 'get me here by [X]AM/PM' option, or the ability to sort flights by time a-la Hipmunk so that if I'm looking for a connecting flight which is different to the recommended one, it's easier to find.