I've googled the net high and low but was unable to get some hints on J2EE performance on different CPU architectures, ECPerf seems to be dead, SPEC results are sparse, etc.
Intel charges and arm and a leg for CPUs with the same clock speed but larger Caches, e.g. Dell charges up to several thousand dollars more per (!) CPU if you're choosing a Xeon with 8MB 2nd level cache instead of 1MB (the later is in fact a plain Desktop P4 with dual CPU capability).
On the other hand JVM benchmarks suggest that current JVM do not profit from 64bit extensions, see http://www.shudo.net/jit/perf/ as an example.
Has anyone done some performance benchmarks for classic 3-tier J2EE applications on standard x86 desktop CPUs and compared them with those - quite expensive - 64bit large cache server CPUs (especially with database running on other machine).
Depends on the app; usually most app servers that talk to the DB are I/O bound and memory bound, not CPU bound.
I would probably go for a large amount of memory and cache. If you go with a 32 bit platform, you're limited to 2 or 3GB for your JVM. Those benchmarks are largely for apps that are CPU bound.