I would honestly like seeing if a representitive sample turned up more malware (in the broadest definition possible) in unofficial sources versus official ones. I don't have any experience with it really, but I figure that the rate of tampering in unofficial distribution must be overstated, because it is still so popular even among the computer-savvy.
Almost all official games nowadays come with what fits the traditional definition of 'malware' compiled in. Most (but not all) of these portions have to be deliberately broken for hassle-free unofficial distribution, and I would imagine that the vast majority of people who do this refrain from re-infecting it with something worse.
Of course the upper bar on severity of adulteration is higher, but the basic point of most of the modifications made IS to remove spyware and functionality-hampering code.
As someone who pirated a lot in the past, I have to say that unofficial (pirate) releases are generally clean (free of virii and malware), and without the issues that DRM cause, as it is almost always completely removed. That being said, I've bought more games this year than I had in the previous five, though for the most part, I almost exclusively play indie games nowadays. Nothing in the mainstream market really appeals to my interests anymore.
On-topic:
Was driving through town, running over the hoards in my truck, when I hit a trap cluster laden with landmines. It blew out enough tires to disable my truck and I was quickly torn to shreds by the resulting influx of zeds attracted by my engine and the explodeys..