Yah, what boom said. That's what I run, baffle pulled (with a Phoenix spark arrestor), PCIII, ProDesign intake. It won't make as much power as the straight-thru exhaust, but it'll be quieter and you don't have to re-pack it, two big pluses for me. And it definitely makes more power than stock. I like the sound, louder than stock but not crazy loud, and the sound dampening won't degrade like when your packing gets compressed/burnt over time in a glass-pack (important to keep the neighbors/other trail users/rangers happy). I had my stock muffler ceramic-coated and it looks great! I just wish some aftermarket made a tuned/chambered exhaust (like a Flowmaster is designed) for my quad. That would be the best sound/power/maintenance compromise for me but most guys want the maximum power they can get with less regard to other issues so there probably isn't enough of a market for it. But spend the money on a PCIII before you run it w/o the baffle. Gotta protect that motor! Jamie at FuelMoto sent mine with a custom map to run with the lid on but I'll try it later with the lid off. Tell them you're a Raptorforum member and they'll sell it for 259.00 delivered, loaded with your map. (That happens to be their reserve price on eBay.) If money isn't the object, more power can be had with an 11:1 piston (still runs on pump gas, but has to be premium) a stage one webcam, and a mild port job. The power gains from these mods won't be as great as they would be with the straight-thru exhaust, but if your priorities are noise control and durability/maintenance w/o regard to cost, that's as far as you can go. A guy could find a way to adapt (weld on mounting brackets, etc) a Flowmaster DeltaFlow 50 Series (or some other car muffler) with an aftermarket Raptor header and mid-pipe (larger pipes/outlet) for more power w/o the noise, but we'll want to see the pictures! (Yes, this is my eventual plan, call me crazy, you won't be the first.) Then again, if it's the $ alone, what boom said.
Yah, size is an issue. There are some smaller ones (Hooker Aerochamber, Flowmaster 40 Series, Edelbrock SDT Series) that might work better. The greatest difference in proportion (compared to stock) would be the width, but if you mounted it horizontally it should fit. The case size of the 40 Series is 4 x 10 x 13, 50 Series is 4 x 10 x 17. Magnaflow has a 4 x 9 oval chambered muffler (still kind of wide). The stock muffler case is 4 x 6 x 16. I would really just like to be able to buy this type of muffler (high-flow, quiet, chambered) made to spec for my raptor, but the lack of one may not stop me from experimenting. Appearance may suffer, but they do have them in stainless steel, and with dual outlets (which might help the look of the wide proportions). I'm just sayin'... it could be done....I didn't say it would be easy... or be good-lookin'....or a smart decision.... hey, Vonage! Sweet!
When the 660s first came out I made a custom chambered muffler for a buddy that bought the first one in the area and it was boomy and throaty. I contemplated building me one for mine but I jump too much and will pop the bottom of it with my caliper like I have my last muffler.
Yah, a modified Flowmaster Hushpower II is maybe the only chambered hi-flow exhaust that could reasonably be made to fit to clear the caliper and tire at full compression. It's case is 4 x 5.5 x 18 (about the same as the stock exhaust), made for street rods. I'm going to e-mail FMF and ask if they might ever offer a version of their Powerline exhaust (mechanical baffles, no packing) for sport riders who want good noise suppression, but like I said before, there's probably not enough of a market for it to make it worthwhile for them to manufacture. Btw, Hpd used to have an exhaust system for the Scrambler 500 that used a Dynomax SuperTurbo muffler. Ugly as can be, I wonder if they sold any....