RSA Dongle Alternatives
 

Are there any cheaper or open source things similar to the dongles? I'm thinking something that uses a regular usb dongle with an app?

At least to my way of thinking, open source dongle is kind of an oxymoron. Maybe if you explain what you're trying to accomplish we can point you in a better direction.

I'm looking for something that changes the root password following some pattern, that only the USB dongle knows.

I've had some serious issues with someone getting my root pass by sniffing.

I'm not aware of any alternatives to the RSA system. What are they sniffing to get your password? It sounds like you have bigger problems.

I agree with Matir, a dongle is the least of your worries. Could you provide a description of how you access the computer and how you think you are being sniffed? One thing to consider is that if they have had root access, they have probably left ways back in that changing root's password won't affect, so you may be looking at reinstalling from clean media.