The Bicycle Wheel Warehouse suggestion by Mobile 155 is a good one. They make good wheels for a nice price. Look around the site for several options which they group by rider weight recommendation.
http://www.bicyclewheelwarehouse.com...0c/cat_43.html
Another forum where you can get good info is
http://forums.roadbikereview.com/wheels-tires/. Many good amatuer and pro wheel builders will offer great advice if you ask, including specific recommendations of rims, hubs and spoke type/count based on your budget, your weight and intended riding style and conditions. The BWW site mentioned above is a sponsor and participant there.
Whether you would realize significantly easier climbing from a new set of wheels is debatable (I don't think so), but a well built wheelset can make a big improvement in how the bike feels and looks. And you could get that for well under the $1K you mentioned.
Not sure what bike late thinks you are riding, but the
Trek Madone 4.5 sure looks to me like a bike suitable for riding fast.