If I'm deploying to servers with WebSphere 6.1 (Java 1.5), should I use IBM's JDK on my build box? Or will Sun's JDK compile to the same binary?
If I should use IBM's, where can I get the Windows x64 version?
I would as much as possible try to keep development as close to production as possible. Ibm and Sun's JDK's certainly both satisfy the SDK certification, but they are by no means identical. Their instrumentation and memory management are at least slightly different. If nothing else, the bugs in the JDK will be different, which your code may only trip over in one scenario vs. another. It'll also probably only happen at 4 am, and when the moon is full especially when you have company over.
I can't tell you where to get IBM's jdk, but if you've got a license to websphere at your company, you should have a contact at IBM to get you a link to that JDK.
Good luck, and always try to minimize differences where possible.