What is a projector's "pixel frequency"? I am looking at the specs of a BenQ projector and trying to understand it's output frequency. 

On page 74 of the manual, there are specs for vertical, horizontal and "pixel" frequency. What does pixel frequency mean?
Pixel frequency, also known as dot clock is referring to the bandwidth of the projector's controller chip.

For a resolution a certain data rate is required to display all the data (not pixel frequency, see later) - it can be for example:

A resolution of 800x600 at 60 Hz would require:

800 x 600 x 3 (RGB) x 60 Hz/2 (interlaced frame rate) = 43 200 000 bytes per second


or divided on 1024^2 = 41.2 Mb/s, as data rate with full 8-bit color-depth.

To calculate the projector/monitor's bandwidth you will need accurate timing measurement available, but you can get close by using the vertical frequency and compensate for VBLANK (vertical blanking which is a sync feature) with about 5% and HBLANK with about 30%:

So with 800x600 resolution at 60 hz:  

800x1.3 x 600x1.05 x 60 = approx. 39 Mhz


The closer these two results get the better it is as that will tell that the projector/monitor is capable to handle the needed data rate to get full resolution, color depth as so forth.

The bandwidth becomes a factor when showing video in particular.