Thought I would provide the definitive answer, now that I see how the points posted after the fact. The answer is that Virgin America, to allocate the base fare, used the miles flown as a percentage of miles ticketed and then multiplied this percentage by the base fare.

That's interesting. Do they also calculate the amount of refund you are due the same way? I wonder if it's ever cheaper to buy A->C with a connection in B and cancel B->C than it is to just buy A->B? Particularly if you're not on the hook for cancellation fees (due to flying F or using the VX premium CC)

I don't believe they use this method to calculate the value of subsequent segments.

I had a LAS-SFO-SAN connection yesterday and, in light of the awful SF weather, wanted to cancel the SFO-SAN segment because the delayed flights rendered the purpose of going to SAN moot.

The agent was unable to get the second leg refunded easily, because it kept saying that the value of it was $0. She was unable to determine the value of the second leg. Indeed, it was much cheaper ($262 total) to fly F from LAS-SFO-SAN than it would have been to book the two segments separately (they would have been $230-$257 each leg). Fwiw, these were all the cheapest F without any promo codes. I ended up getting the flight re routed to LAX because it was a suitable option.

Was there any extra fee in the re-route? I'd be curious to know how many points you end up getting when they post.

No, they did not charge any fee for the reroute. I was pleasantly surprised; I'd have been more than willing to pay a small SDC fee or something. The agent was very accommodating. I actually had two PNRs: one for LAS-SFO-SAN on Day 1 and another one for SAN-SFO-DAL on Day 2. The extensive weather delays caused me to miss my meeting in SAN. The agent changed the first PNR to LAS-SFO-LAX and the second PNR to LAX-DAL. We came to the agreement that this was probably best because it prevent me from having to come back to SFO on the second day and get subjected to weather issues again, and it'd also "protect" my flight to DAL by increasing the odds of it arriving on time. I'm used to (spoiled by?) good service from VX, but modifying two PNRs to have not only different routing but also city pairs is impressive -- especially without even a Same Day Confirmed Change fee. It's rare that airlines are willing to make such changes based on weather delays alone.

My points for LAS-SFO-LAX posted today. The extensive changes to the PNR must have screwed something up. I was supposed to get 1110 base points + Silver Bonus + Triple Points for First Class. Since there were two segments, I was expecting the 1110 points to be split into two entries (proportionally based on miles flown, as Colin mentioned). Instead, ended up with 1110 base points for each leg -- meaning I accidentally got double credit for the PNR! I'm unsure if I should do anything about it... ;)