Modifying your exhaust is one of the BEST modifications you can do. The 5MGE is naturally choked down, so anything you can do to free up the air flow IN and OUT of the engine is a GOOD thing.
RabidChimp.com - Second Generation Supra 3" Mandrel Bent Cat-Back Exhaust
Tossing the exhaust manifold in exchange for a header at the same time you upgrade the rest of your exhaust will net you the biggest gains.
RabidChimp.com - Modified Pacesetter Header
I have a Trust header with RabidChimps 2.5" catback & Magnaflow muffler. You can hear it in this lame video I made awhile back:
Video of My 5M - Photobucket - Video and Image Hosting