I would definitely check out local humane societies and animal shelters to see if any of them microchip. Chances are the cost will be significantly lower. The shelter that I work at charges $25 for chipping a public animal (every animal that we put up for adoption is chipped and the cost included in the adoption fee). It might also be handy to find out what kind of microchip scanners the local shelters use. There are a number of different microchip companies, and 3 different microchip frequencies (125 kHz, 128 kHz, and 134.2 kHz) used in the US. The 125 kHz chips are more common, but the 134.2 kHZ is being seen more and more (134.2 kHz is the International standard). Not all microchip scanners can read all microchips, so getting you cat chipped with one that the local shelters can read would be a good idea. Different microchip companies have different registration fees (one-time fee, annual fee, life-long fee, etc.), so you could also contact different companies to see what they are. Also, some microchip companies allow you to register chips from different companies with them, so you can keep all your information in one place.
With regards to the microchipping itself, it is done subcutaneously with a large-grade needle in the scruff of the neck between the shoulder blades. Most cats don't even seem to notice it being done. Since they are done SubQ, microchips have been known to migrate a bit (for example, ending up down near the shoulder or further down the back).
Two things that I would strongly urge after you have your cat microchipped:
1) Be sure to have her scanned a few days after the implantation. It's rare, but occasionally microchips do slip back out of the needle hole before it heals.
2) Even if your vet or wherever you have her microchipped at does register your cat, be sure to call the microchip company yourself and double-check that the registration has worked and the information is correct. And make sure to update your information with the microchip company whenever it changes. We often have animals come to our shelter with chips that were never registered, leaving us with no way to find the owner.