Since the output of a QTR-RC sensor is a digital pulse, you can take all of your readings in parallel. The mega168 only has one ADC, which means you can only read one analog voltage input at a time, so you would need to process QTR-A sensors sequentially. On the 3pi, the line sensors have an even faster response time than standard QTR-RC sensors, producing a 250 - 500 us pulse for black and maybe a 40 us pulse for white, which leads to a potential five-sensor sample rate of 2 - 4 kHz.
Additionally, because of the greater noise immunity of the RC version, you don't need to average readings to filter out noise. The QTR-A version, on the other hand, is succeptible to noise, especially if you are driving motors, so you would want to average several successive readings together before relying on the output.
You can see a not-so-high-resolution view of the bottom at the start of the 3pi maze-solving video (make sure to click on "watch in high quality" link). The line sensors are curved along the underside of the front edge. If you look at the picture of the top side of the robot, you can see schematic symbols in the silkscreen that show the locations of the sensors (there are three somewhat close together along the center portion of the front with one spread farther to the left beyond the left set of 8 prototyping holes an one spread farther to the right beyond the right set of 8 prototyping holes). We will release some better pictures of the 3pi soon!
We will also release some line-following and maze-solving code with the 3pi, but we don't have anything specific we want to make public yet. If you want to see a slightly higher-level version of the code running on these line followers, take a look at the third sample program on this page:
If you pick the proper constants Kp and Kd, you pretty much have the line-following code that is running on the 3pis in the extreme line following video (it really is that simple).