I think I'm going to have to say that my favorite section is either Secsech/SF Salmon as a 3 day trip or Big Sands Creek up by the Lochsa.
Sesesh/SF Salmon because its 3 great days on the water with great camping. You start off on a creek essentially and end up on one of the biggest rivers in the state, traveling something like 60 or 70 miles then the shuttle is only an hour. Its pretty cool.
Big Sands Creek because its super steep, with cool bouldery/bedrock drops. It has a 3 mile hike in through the selway wilderness area and when you are in the canyon, you are in the middle of no where running some crazy gradient. Its really kind of scary but fun.
Tough call. Secesh? S. Salmon? N.F. Payette? Lolo Creek? Selway? All classic Idaho runs. But the Secesh and turning the corner onto the S. Salmon as Copeland says is probably one of the greatest wilderness runs in the lower 48!