Dabrowski and Munson weren't able to reproduce the old 50- or 100-millisecond rule of thumb in what sounds to me like a poorly-controlled experimentIt sounds rather poorly-controlled to me too.
They mention that they didn't account for the time from mouse-down to mouse-release. Seriously? Here is a program that can measure that difference: http://www.daimi.au.dk/~sandmann/click.py. It uses GTK+ so you'll probably need Linux to run it. For me, the delay seems to be around 30 ms. They also don't mention the framerate of the screen or whether they controlled for that. On a 60Hz monitor there is a delay of 17ms between frames.
Both 17 and 30 ms are huge numbers if you are measuring intervals on the order of 100ms.
Then there is the question of what you consciously perceive vs. what you subconsciously perceive. It would surprise me if you couldn't measure a difference even in cases where the subjects didn't notice anything themselves.
Finally, we can definitely reject the idea that latencies below 100 ms never matter: there is an obvious difference between a 10 fps animation and a 60 fps one.