Apart from stronger ALSR entropy...
Is a system using amd64 any safer than 686-pae?
What are the advantages, if any?
In general, yes, using 64-bit architectures is a bit safer.
ASLR (Address Space Layout Randomization) is a lot more effective on 64-bit architectures. On 32-bit architectures, ASLR is not very effective. On 32-bit architectures, it's only possible to introduce a half a dozen or a dozen or so bits of randomness into the address space layout. This means that an attacker can defeat ASLR by simply trying many times (a few hundred or a few thousand times).
ASLR makes it harder for an attacker to exploit buffer overrun vulnerabilities, so this difference between 32-bit and 64-bit architectures has some relevance to system security.
Apart from its effects on ASLR, I'm not aware of any security benefits of a 64-bit architecture over a 32-bit architecture.