I'm currently building a capactive measurement system as part of my PHd, I've found, depending on what accuracy you want, that the best way is to use a sigma delta modulation technique. You can find this in Analog Devices AD774x series of Capacitive to Digital Converters. These chips go from one channel to 12 channels for mounting capacitive electrodes and have resolutions between 8 and 24 bits over full scale ranges of around 25pF with a bit of calibration, obviously, that gives a lot of sensitivity.
The chips communicate with a host through the i2c bus, so you ca use Arduino's wire library to get the data out of the slave chip (I sweated over a prototype function for a PIC i2c protocol for months when I found arduino!) and use that to manipulate the data anyway you want.
the only thing is that these chips are only available in TSSOP form so can be a bit of a pain in the arse to solder, however it's quite a nice solution as I am finding out.