So you’re looking at a stock Crystallyte controller. It’s $150. You’ve heard they blow their FETs easily. So, you think, “I can build one better.”
Maybe not, but I thought so. I thought I might be able to pull it off cheaper. If not, at least it would be worth the experience.
Well six months later I’m not quite done and I can tell you that it might be better, it was definitely not cheaper, and the jury is out on the experience 
I am still currently working out the bugs in the controller. The parts did indeed cost less than the controllers out there; but the trial and error of assembling it meant spending more. If you’re only going to build one or two, it’s not cost effective. It takes unusual requirements or volume to make it worth the effort.
Getting Started
The general idea is to use the Pulse Width Modulation features of a microcontroller to drive six MOSFETs attached to a brushless DC motor. This is the most practically efficient set up.
There is a wealth of information on the internet about using PWM to control motors. Just start Googling; you’ll find some simple explanations.
Since I have familiarity with the Atmel microcontrollers, I went with those. Atmel has several application notes for motor control that include code that makes getting started easy. I recommend AVR447, as this uses the cheap and commonly available ATMEGA88 and 168 (the note says it works on the ATMEGA48 too, but I could never load the included code into the small program space of that chip). Also, the notes are superior to some of the other examples. Unfortunately the source is written for an expensive commercial compiler; but editing it to work with AVR GCC is not too difficult. The greatest problem is in changing the syntax for storing arrays in flash memory into the format expected by AVR GCC, then using pgm_read_byte to read from flash memory (the commercial compiler is smart enough to automatically do the read for you). Also, the ISR names differ. I’d post the code here, but I’m not sure of the licensing.
AVR447 is based on using the Atmel motor control evaluation board. Since I haven’t got one, and anyway, it is built to drive a small fan motor, it would not work for us anyway. So we are on our own there.
But there are a lot of schematics you can find on Google too. Just search for “H bridge schematic.” An H bridge uses two MOSFETs linked end to end. The motor connects in between the two MOSFETs. One MOSFET is connected to supply positive, the other to ground. Control circuitry alternates which of the two is on. This alternation creates a wave that makes the motor spin. Many of the H bridge schematics use circuits with high parts counts. The easiest way to go is to find one that uses an integrated high/low side driver. International Rectifier makes a slew of these. Look for IRF2101 for example. You can substitute other chips, just make sure the logic input level matches your chip. On the supply side, all the chips seem to be rated up to 200V or 600V, so that should not be a problem. The only other differentiation among these chips that I can see is that some have inverting inputs. You can use these, but then your software must be written for it.
Here is a list of IRF hi/lo side driver parts: http://www.digchip.com/datasheets/parts/ir/parts_ir02.php
Get DIP package ICs if you can. These converters from SOIC to DIP cost $5 each. I clicked on the wrong item at Digikey…