Well I've only seen season 1 & 2 and I'm still finding it hard but here goes:
(Not In Order)
Phase One - Just AMAZING! especially since it was mid-season
Truth Be Told - The episode that kicked it all off in style!
The Enemy Walks In - Say hello to one of the best characters on Alias - Irina!
Almost Thirty Years - A great finale to a brilliant season 1.
Truth Takes Time - A brilliant episode, Irina rules and poor Amy
The Box parts 1 + 2 - Great story, great guest stars!
The Telling - Probably my favourite episode so far!
Passage parts 1 + 2 - The Bristow family, kicking ass!
A Dark Turn - Irina = Brilliant! Great and dramatic!
Endgame - I loved it and Tracy Middendorf guest starred!