The former NBA referee has written some remarks about the biases of NBA refs, that, if true, would be quite damning. Apparently some refs bet on who would be the first to call a technical foul in a given game! More troublesome are the systematic biases, like the favorable treatment of Kobe or pushing a playoff series to seven games on purpose. But are his allegations likely to be true? Let's evaluate the evidence:
In Donaghy's favor: The details he lists seem too exhaustive and specific to be completely fabricated; Heat-Mavs, 2006 finals; former FBI agent Philip Scala's endorsement; the fact that the NBA has a huge public relations incentive to make his allegations appear false; if any of the specific allegations he made could be proven false it would be a huge blow to him, yet none of them have been.
Against Donaghy: Random House/Triump books canceled publication of his book after an apparently independent review process; the NBA denies his allegations; he stands to make a profit from book sales and potentially a higher profit if the claims are more outrageous; if "everyone was doing it" then he looks less bad to the public in comparison; the NBA claims that the FBI found no other "criminal conduct" among other referees in its review, although some of the stuff he alleges may not be criminal per se as much as it would be unfair.
When Jose Canseco made his allegations about steroids in baseball they were at least verifiable in the long run, as players could recieve blood tests for steroids. Donaghy's biggest problem seems to be that he has no similar way to prove his points--unless he can convince other referees who also have an in to corroborate them.
Tim Donaghy could either represent a case study in libel or a case study in how a large group (i.e., the NBA admin) could keep a secret. I think it is more likely the latter with a probability of about 80%. So I'd bet 4-1 that yes, most of what he says is true, if you could find some way of verifying it. If he is indeed telling the truth, the fact that Random House canceled publication of his book shows how defecting from the group and revealing a secret via a tell-all book is much harder in practice than in theory. Telling a secret really is hard. This makes other conspiracy theories seem more likely, too.