None of these are, ironically, factions I am or was involved in (I'm not really a member of any faction), but they've grabbed my attention for varying reasons:
Agents of Chaos upset the status quo and brought a new approach to messing with big blobs on the map. Which is good.
One Sith was neat. An invasion machine that shook things up by a ton.
Darkwire brings a whole new genre to Star Wars, yet in a manner that doesn't appear alien or out of place.