People can charge what ever they want to for the same thing..so some variation is just due to supply/demand.
Some parts are stainless steel, some are anodized aluminum...the SS is more expensive...and, there are differnt grades of SS as well, so even that can reflect the better/worse metal quality.
Some have thicker or thinner metal sheet, so the thicker metal is more expensive.
Some have a larger diameter, or a smaller diameter..the larger diameters tend to be more expensive.
Some have simple glass packs inside the mufflers, some have more expensive steel baffles, perforated plates, etc.
Some are tuned to alllow maximum flow/noise, others are designed to pass noise emissions standards, let you sneak home after a night out with the boyz....etc...
The compromise between noise/power costs $ to achieve both ends.
Even within a brand (Magnaflow, Dynomax, Gibson, Borla, etc...), they will have different versions of the same thing...so one Magnaflow might be $400, another Magnaflow might be $1,200, etc.
As there are A LOT of variables, your best bet is to pick a brand to start with, and go to their web site, and read what they say about their stuff.
Most have sound files to let you hear what they sound like, and charts with noise vs power curves, options, etc.
Read up until you understand what you need to to make an informed decision...and then go to another site, rinse/repeat.
The second site onwards will be easy compared to the first one, as the concepts will be already there, and only the brand's options and features will be new...
And,
its those options and features that you will be comparison shopping.
Enjoy!
(Or, you can read a bunch of posts from people here saying I got a So and So and it Rocks! - and just randomly pick one too)