The BG-42 Military costs about $50 more than the standard S30V. For that $50 you get: (1) BG-42 blade; (2) carbon fiber scales; and (3) a sprint run knife that may not be made again.
1. The BG-42 blade. I have several BG-42 blades, including a recently-aquired BG-42 Military. I have never run tests, but my subjective imopression is that BG-42 and S30V hold an edge about the same length of time. BG-42 seems to take a finer edge, but again that's subjective. Some people favor BG-42 over S30V. For example, some Sebenza folks prefer the older BG-42 knives. But IIRC, they usually do so on a fairly subjective basis. I think however you stack it up, the steels are roughly on par with each other -- at the very least BG-42 is not vastly superior to S30V. Some people also like to have something that's a little different than most other folks. BG-42 gives you a small dose of that.
2. Carbon fiber scales. My understanding is that carbon fiber is stiffer and stronger than G-10. However, I've never heard of a Military G-10 handle breaking under normal use or otherwise. There was talk of the older ones flexing, but I believe Spyderco addressed that years ago.
3. Sprint run. There are far fewer BG-42 knives available than the S30V ones. Does that make it more valuable? I reallly don't know. But I do know the BG-42 sprint run was released in 2006, and they are still available new at at least one online dealer as of today. So it's hard to say the demand has been high. But again, it's not like what everyone else has.
Given all that, I think the S30V version represents the better value for a user. If your a Spyderco nut or you just like to collect different versions of the Military it makes more sense. I'd also look at the S90V version for a mere $25 more, provided you either already have or are willing to invest in diamond stones.