CPU wise they are pretty close really in performance in most scenarios. Hyperthreading won't do you a ton of good in most of your proposed use cases especially with that many cores already... but E7540 runs on qpi link which is faster and has a lower tdp and is newer so the motherboard may have better features? On the other hand the X7460 has more cache and is clocked higher, and comes with way more memory, so much more so you could run things on a ramdisk with little effort which could be nice.
Assuming they cost about the same, it comes down to the motherboard I suppose.