The TV show White Collar's pilot has a cool depiction of Neil Caffrey copying a guard's magnetic stripe badge using a tape deck by recording it to tape, then playing it back through the record (write) head on the other side of the tape player while he slid a new card through. It would be hard to get the timing right, but there's no reason this shouldn't work.
It's incredibly primitive technology, as is simple RFID - the cloning process isn't much more difficult. Fortunately my university uses HID iCLASS contactless smart cards - there is actually a cryptographic handshake between the reader and my student ID which is resistant to replay attacks. If implemented correctly, it's impossible to copy the electronic access control portion of a student ID without the university's private keys. (The same access control infrastructure that's on my dorm's main entrance also guards healthcare information, nuclear and virology labs, etc. so that makes sense.)
Best I can find so far is this website which kind of describes what is going on:
This is more of the way it works:
> Magnetic stripe cloning can be detected by the implementation of magnetic card reader heads and firmware that can read a signature of magnetic noise permanently embedded in all magnetic stripes during the card production process. This signature can be used in conjunction with common two factor authentication schemes utilized in ATM, debit/retail point-of-sale and prepaid card applications. -- http://en.wikipedia.org/wiki/Magnetic_stripe_card
It might work like a bunch of tiny electromagnets appropriately arranged on the back of the card, like pixels on your screen. These electromagnets can probably be polarized in a particular way to match the original card.
This was a crude first pass, which is evident from the fact that the shim is a sawed off kitchen knife. In principle if you make the electromagnets smaller you could fit three. Make them adequately decoupled and you're away.
If these guys have an alternative approach I would be interested to read about it, but as far as I can tell they don't describe the method anywhere.