The wife rides 2009 Fuji Newest 1.0 which came equipped with Tektro R350 brakes. Stopping her bike (especially on a fast descent) is a bit of an adventure compared to stopping my Trek (with Ultegra 6600 brakes).
Here's what I've done:
1. Had the LBS true up the wheels. They were both a bit wobbly, so the pads had to be run pretty far from the wheel.
2. Gave the pads themselves a light sanding with 600 grit sandpaper (to remove any glaze)
They still suck. A Kool Stop Dura cartridge conversion would set me back about $40 or I could get a "new old stock" (NOS) of Shimano 105 5600 brakes for $60. Any reason to not get the 105 brakes?
One annoying thing about the Tektros is that the right side pad is not parallel to the wheel. Only the front half of the pad actually does anything. It doesn't look like it's a pad issue because they are fairly new. It looks like the caliper arm needs to be bent.