From a Java perspective that should not matter - Java code is Java code - whether built on a 64-bit system or 32-bit system, it is all the same.
However, the 64-bit JVMs do seem to introduce all kinds of issues. Running a 64-bit JVM on 64-bit Vista, I had all kinds of problems with Eclipse 3.3 itself and with JBoss Tools. Eclipse 3.4 seems to be better behaved on 64-bit systems, though tere are still a few quirks. On my 32-bit systems, however, Eclipse 3.3/3.4 and JBoss Tools work just fine.
And I should point out that I ran into the same issues running Eclipse 3.3 on 64-bit Kubuntu 8.0.4 with both a 32-bit and 64-bit JVM. Eclipse 3.4 seems to work much better there.