I'm completely confused by Intel's naming system. I understand what makes Xeon E3 different from i5. But what, for example, makes the Xeon X3440 different from E3-1230? (Apart from clock speed).
Loads of stuff: http://ark.intel.com/compare/42928,52271,65734
Whether any of that (core architecture, manufacturing process, power consumption, socket, RAM speed, etc) is important to you, well, that's up to you.
If you are looking to replace a CPU in a board you already have, then you don't really have much choice (X3440 is LGA1156, E3-1230 is LGA1155). If you're looking at a whole new setup, I would strongly recommend going with the newer technology.