Komes,
I ran Ubuntu 6.06 64-bit for about 3 months. The 64-bit build of Eclipse using the 64-bit VM from Sun was flaky at best… I wouldn’t suggest it. Just grab the normal 32-bit build of Eclipse with the 32-bit JDK from Sun and use MyEclipse on it, it will run fine.
Also, don’t use the custom Eclipse build from Synaptic, I had problems with that build, some crashes and instabilities… not sure why.