Great thread to give a bump to. My list is bands who have IMO moved prog rock on, rather than re-cycling older more traditional prog rock sounds and sub genres. My favourites of a rather eclectic selection are
Riverside - as already recommended
Porcupine Tree - again as recommended
The Flaming Lips - totally out there, genre bending to the point of being progressive progressive rock.
Jah Wobble - in his various incantations and collaborations.
Mercury Rev - etherial, melodic, very imaginative.
Cornelius - Japanese sound master.
The Beta Band - heavy modern prog rock with a twist.
Tunng - described as folkatronic, to which add very clever and wistful.
The Pineapple Thief - as previously recommended.