Assuming you can't do this job yourself (it's fairly easy especially if you have a friend helping) $350 for just replacing pads is kind of high IMO. At a garage they have the means to do a job like that with just one guy in probably <2 hours. OEM pads can't cost more than $80-100, so that price seems high to me.
If they are replacing rotors, then price seems right.
Mechs are often paid flat rate and not hourly. Flat rate is calculated by averaging the time it takes for "all" mechanics of various experience to perform the job. The job does not have a regard for obstacles, like rust keeping the wheel on. Labor rate is hours multiplied by price.
http://www.brakepadscostguide.com/
http://cars.costhelper.com/brakes.html
The spread is pretty wide, and the these sites report $300 figure is within the spread. Since the original poster mentioned that the quotes he got were for both the front and the back, $350 is actually on the lower cost side.
It pays find out who is the OEM manufacturer of your make's brakes and find out their OEM equivalent line. Like Akebono's ProACT Ultra Premium line should be the brake pads Toyota and Honda rebrands and then sells at the dealership at a huge markup. The ACT923 is likely the OEM pads that come with a Toyota Matrix, for example. Taking advantage of coupon codes at Advance Auto online also can bring the cost down further.
Many brakes are easy to do and the cost of labor could have been used to purchase tools and supplies. I am suspicious of mechanics and don't want to feed a possible bad egg with my money for the simpler tasks like many brakes. But the labor costs are somewhat justified. They had to get an education, buy expensive tools, and use powerful impacts and lifting equipment to get to that level of speed. If someone doesn't know how to do something, they gotta pay someone else who does know how to do the job.