I'll second Filtersweep's suggestion -- if it were to be custom, threadless would be my choice. But...

Aesthetically, it depends. I have a threadless set-up now and I love it. If I decide to build up another bike, it might be threaded, since I may be building it in a certain aesthetic and style (more old school) and for its use: track only.

My threadless set-up is 1". To match the slimmer tubing of a my steel frame, I managed to find a Salsa SUL stem that fits the paint job as well.

Here are some photos of my set-up: