You and me both! Just called up some local shops this week to get quotes and such.
Let me say this: getting a new exhaust fabricated from a muffler shop is cheaper than buying a full exhaust online. As in up to $300 cheaper. For a stock 4Runner, you can get new piping (go up 1/4 if you want) and a new muffler, such as a Magnaflow or Dynomax, starting at $250. Some will even put a tip on for that price. Don't bother with mandrel bent piping or nothing like that, you'll never see the difference on a stock engine. Also, any muffler shop will be able to weld in a new bung for the O2 sensor really easy.
Here's what I've learned after searching online about muffler brands (and talking with exhaust shops). All the major brands, Magnaflow, Borla, Flowmaster and Dynomax will increase flow and sound over a stock muffler. Flowmaster has the most restrictive out of the four, meaning less HP gains. The other three are pretty much completely equal. Dynomax is louder than Borla and Magnaflow, with Magnaflow being the lowest frequency.
As far as types of mufflers, the three (Borla, Magnaflow and Dynomax) have a "touring" or "economy" version that reduced the sound the most, but still louder than a stock muffler. Borla and Dynomax also have "performance" mufflers that do nothing at all for performance on a stock 4Runner, only make it louder. This is not my cup of tea so I'm staying away from those.
I've got a supercharger so I'm a little more picky. I have a much higher exhaust flow rate (my 4Runner spews exhaust like no other) so I am looking at mandrel bent piping as opposed to crush bent for a performance gain. I am also building the engine up to hit near 300 hp at the crank... so it's a different route for me.
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