<p>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?</p>

<p>If I should use IBM's, where can I get the Windows x64 version?</p>

It should not make any difference. It will probably not be exactly the same binary but 100% compatible. I assume you're using external libraries anyways like log4j or maybe hibernate or whatever and those are not built using the IBM JDK.
There are differences in the JREs, however. For example, I remember that when I listed methods or fields of a class using reflection, the IBM JRE used to give them to me in a different order than the Sun one.