A very personal list - as favorite spots to fly fish should be. Ask me tomorrow and this list will change.
South Branch Raritan River, NJ - my home water with beautiful wild browns
Skaneateles Lake, NY - best mixed bag lake (can catch landlocked salmon, lakers, rainbows, yellow perch and smallies in the same day) I know and a beautiful place
Centre Co. PA limestoners - classic fly water, plenty of trout
Connetquot R, NY - my favorite fishing "Disneyland"
Southwest Corner of Newfoundland - down home Atlantic salmon fishing at its best.
The Zen answer is always best. Favorite spot - where I'm fishing now, Favorite rod - the one in my hand, favorite fly - the one I got on etc, etc.