I think something interesting could be having augments & sets that are linked to faction favour - have certain augments available via a special vendor for each one when you hit a specific favour level (say 2nd for some, maybe 3rd for others) that are themed to match with the house, eg. house phiarlan could have a diamond that boosts saves & DCs of illusion spells as well as another that boosts both search & spot skills & another that boosts hide & move silently, but balance them by being a lower boost than is available via 2 separate regular ones.
Another idea could be augments that grant a set bonus (these are already present linked to raid gear I know) when slotted in gear, they'd be more easily accessible but again that could be balanced out by making them a little less powerful than the stuff that requires very specific gear setups. You could also have an additional effect that grants extra bonuses (similar to chimera's fang & it's dragonmark bonuses) if you have the appropriate favour level with that faction (link it to the +HP feat) as a whole "hey, you're flying our flag" kind of thing & it'd encourage people to play more variety of quests.