And they have a pretty decent new album (out last year) that is a rock opera of sorts along about "New Roman Times" I haven't listened to it enough to have a sense of it as a totality, but it has some good tracks in terms of both music and politics.
On the alt country front, add My Morning Jacket and Band of Horses. Though Wilco is still the top, even though some of their best stuff has come from their departure from Tupelo/Sun Volt stuff. And Following from this, Jeff Tweedy, lead singer of Wilco has a side project called Loose Fur and they have an entertaining (and quite good musically) album called "Born Again in the USA."
Wilco also has a fairly progressive stance on the intellectual property issue, precisely because their big breakthrough album wasn't really released on a major label--or at least it wasn't released on a major label until well after it had been streamed for months off of their website and leaked to fans in other places. There's more of a story here but there's a documentary about it ("I am trying to break your heart") so you can find out about it yourself. Needless to say, I'm a fan.