My current setup features a mid 2013 Macbook Air which powers 3 monitors (27'' Thunderbolt display and two other pc monitors. Peripheral wise my desk sports a Caldigit thunderbolt hub, a 2 TB backup drive and an addition 1 TB drive for Time Machine backups.
Blarregalia, what are you using to power the other two displays? I'm considering trading my Mac Mini in for an Air, but 3 displays is a big priority for me.
It's my understanding that using a Thunderbolt display kills the HDMI on the Caldigit, but I could very well be wrong. Either way, I'm very curious as to what you're using to run the 3rd display.