I am trying to control 88 electromagnets independently with an atmega 328 powered duemilenove, and don't know how. could someone please tell me a method by which to do this?
You could use 11 595 shift registers to give you 88 digital outs.
See the playground for a "how to".
The problem is that the 595 shiftregisters can probably not source the current needed to drive an electromagnet, so you need to use either a transistor or some darlington transistor arrays. You need to known how much current each electromagnet will draw when engaged.
Look for examples on driving relays with Arduino, it'is basically the same you want to do.
Under all circumstances you will need some kind of external powersupply, and depending on how many of the electromagnets will be on at the same time it might have to be a very serious one.
There is a high power version of 595 specifically designed for this purpose (to drive coils etc): http://www.sparkfun.com/commerce/product_info.php?products_id=734
There will only be about five on at a time, and I will see about this shift register. Thank you!