I put a very high probability that some form of tampering occurred primarily due to the failure of the data to obey a generalized Benford's law. Although a large amount of noise has been made about the the fact that some counties had more votes cast in the Republic governor's race than reported turnout, I don't see that as strong evidence of fraud since turnout levels in local elections are often based on the counting ability of the election volunteers who often aren't very competent.

I'd give probability estimates very similar to those of Jim's but with a slightly higher percentage for people actually voting for him. I'd do that I think by moving most of the probability mass from the idea of someone tampering with the election to expose the insecure voting machines which implies a very strange set of ethical thought processes. I've also had enough experience in local elections to know that sometimes very weird things happen for reasons that no one can explain (and that this occurs even with systems that are difficult to tamper with). So using the primary breakdown given by Jim I'd put it as follows:

* Voters actually voted for him: 0.25
* Someone tampered with the voting machines or memory cards to make Alvin Greene win: 0.25
* ...and that person did it because they wanted Alvin Greene to win: 0.1
* ...and that person did it for kicks: 0.1
* ...and that person did it because they wanted to expose the insecure voting machines: 0.05
* Someone meant to tamper with a different election on the same ballot, but accidentally altered the democratic primary additionally or instead: 0.1
* The votes were altered by leftover malware from a previous election which was also hacked: 0.2
* There was a legitimate error in setting up or managing the voting machines altered the vote totals: 0.2

Edit: Thinking this through another possibility that should be listed is deliberate Republican cross-over (since it is an open primary) but given the evidence that seems of negligible probability at this point (< .01)).