Errant said:
I'm picturing a campaign in one of the Five Nations in Eberron where the PCs are recruited by their realm's spymaster firstly to investigate influential nobles with questionable allegiances. Nobles that may be innocent and too influential to confront directly regardless. Later the PCs will be sent into other realms to investigate links and potential threats to their realm. I'm aware my players like a fair bit of action in their adventures so one or two fights, hopefully out of public view, will be inevitable (or at least highly likely) in each adventure. Successful missions will just mean no-one knows or can prove they were involved after the event.
Well, the Karrns have a lot of messed-up crap going on... and there's stuff in Thrane... and Breland... and, well, there's a lot of messed up stuff in the Five Nations. None of it specifically requires a spymaster to involve a party.
A mysterious patron for a more political/intrigue game does not necessarily have to be a spymaster, nor even beneficial to the realm/nation in the long run (maybe one of the Lords of Dust is screwing around and planting false ideas in the players (especially with Thrane politics), or some neutral-aligned Ilithid with a fascination for human politics wants to play games, or whatever). Mercenaries & swords-for-hire can also get themselves into situations that go far beyond the present knowledge of the mercenary-adventurers - read: knee-deep in a political fight that is way above their heads.
With House Deneith & Blademarks (the primary mercenary guild for the Five Nations), check out the info for them in the Sharn book (if you've got it), for instance. I'm kind of into the Blademarks at the moment, if you can't tell. House Deneith is full of surprises.
And if you can work in the politics of a House, it gives the Dragonmarks a whole lot more form and makes more sense in the longer run IMO... there's something just not quite right when you have all these Dragonmarks getting together for no particular reason, and thus a more House-based game/campaign can eliminate some of that character ambiguity. Maybe think about a dominant House, and what you can do with it. House politics can shake an entire nation.
Eberron is definitely rich ground for an intrigue-based game... you should have no trouble finding inspiration just flipping through some of the books.