As for highway Prius vs. Civic, many have found the Prius to handle better (MPG wise) at 70+
mph, and overall will generally get better fuel efficiency than the Civic, and that's especially true if you decide to hypermile, as the recent 110 MPG marathon proves.
The 2006 should be eligible for the sticker as long as they keep the emissions rating. I haven't seen definitive evidence on the emissions yet, it would be nice if they would just make all the HCH's PZEV like the Prius, but they should at least still
offer it in clean states.