On my commuter I run 700x28 Marathons (HS 368, not Plus, which are designated HS 348). I've had them since early September of last year and no flats; in fact, they show barely any discernible wear at all. (I love these tires; they scream "SENSIBLE!!" To wit: the dynamo strips on the sidewalls, which are a standing temptation to buy a set of generator lights.)

Concerning tire clearance, I think it's worth investigating the Marathons in 700x25. Perhaps someone can say whether they run big for 25s; but I've mounted 700x26s (Panaracer Stradius Sport) without a problem on my racing bike, the clearances of which (particularly at the rear brake bridge) are probably as tight as most anything out there.