If you're going to keep the stock exhaust manifolds I would suggest replacing the restrictive factory y-pipe. If you're planning on replacing the stock manifolds with headers then I would wait to address the y-pipe. Aside from that you could do an air intake, tuner, electric fan, gears, converter, shift kit/valve body, crank pulley, cam. Lots of options. Depends on what you want and do with the truck I'd say. Some of those things I wouldn't do before others. For example i would not install a larger cam in an otherwise stock truck. And there are supporting mods that can be a good idea no matter what you do with the truck like a larger trans cooler and/or deeper trans pan. I'd say generally you want to start out with easy stuff like bolt-ons, then the more in depth stuff like the gears, tuner, converter, cam, etc.
I'm assuming this is a Hemi truck in that reply as well.