What's the best exhaust system upgrade for v6 03 prerunner, flowmaster, magnaflow or some other manufacturer?

depends on how much you want to spend.
i bought a borla exhast system, sounds good
on my 99 tacoma 4x4 2.7 liter. probaly sound
even better on a 6 cyl. i gave $364 for
my system. although you can get a flomaster
put on your existing exhaust for $75 and up.
my truck sounds like the supra from fast and
the furious.

i own a '04 prerunner 3.4v6, and installed both magna and flowmaster. magna flow was really good, deep sound. The flowmaster i installed after was ok, it was deep and had a more garggling sound. As far as performance, you're not going to notice a huge difference, no matter what car or truck you own, or what exhaust system you go with. If anything you're only gainning maybe 2-4 horses (not worth spending over $300-$700 for a name brand system.) So anyways, just change your factory muffler with a magna or flowmaster for about $100 with installation and you're all good to go.