In the order of most to least restriction for individual components (as far as I know):
1) Cats - But you might experience drone or you might fail on the emissions test
2) Rear muffler - The sound will definitely increase if you replace this piece
3) Midpipe Resonator - Small cross section and I believe it's a glass pack muffler.
4) Y-pipe - Normally it's a great restriction and since it's closer to the engine, restrictions on this piece will be felt more. But since is "restriction sorted by components", it's not as restrictive as the mufflers & cats
5) Headers - This is a restrictive piece as well and since it's the closest component to the engine, you'll feel the restrictions on this piece. But as an individual component, again, it's not as restrictive as mufflers
Now, if you're looking for the best performance, we should ask your driving style. If you regularly rev up your engine up to say 5000-5500 rpms, you'll feel more gains from the exhaust mods and enlarging the diameter on the pipes. But if you generally don't go up above 4000 rpms, you won't feel as much. Plus if you're in this second group, you might feel some torque loss if you go with a larger diameter exhaust..
IMO, whatever you do, the best approach is to keep the exhaust pipe diameter at a consistent level (either 2.5" single/dual setup or 3.0" single setup) and replace the mid and rear mufflers with aftermarket ones. If you're going to replace the y-pipe, make sure the collector diameter matches the mid pipe connection diameter. Each and every diameter change will result in exhaust speed loss which in turn will cost you low end grunt.
Here are what I'd choose:
- If you want to upgrade JUST one piece, get the HKS Rear Muffler OR just get the Nismo rear end (if you can find one)
- If you want to upgrade 2-3 pieces but keep the costs low, get HKS Rear + y-pipe.. You can do away with the stock mid pipe resonator in place
- If you want to upgrade 2-3 piece but cost is not that much of a problem, you can get HKS mid + rear, Y-pipe OR you can get the Nismo and get it extended
Stillen is another alternative but IMO it's both expensive and if you go with rear GTSpec braces or a tow hitch, you'll have problems.. Finally, the difference between any of the aftermarket systems are mainly sound and quality. You really won't feel any significant differences in performance. You might feel slight differences between them but nothing major.. Just make sure to keep it consistent so that you don't loose any torque.