Where can I get information on how to implement AES? I want to write AES from scratch without using the built in libraries of java. I know there are hundreds of AES programs (and websites) out there but I can't seem to find a site that gives me the details I think I would/should need to write my own Java program.

I know that AES has S-boxes like DES has. Were would I look for them? Also, I would like more info on the AES "counter mode".
The AES standard is reasonably clear, and (theoretically) sufficient to implement the AES itself. For block cipher modes of operation (including counter mode), see NIST Special Publication 800-38A.