I currently own a number of Canon USM lenses (15-85mm, 70-300mm L, 100-300mm, 100mm macro non L). I also own a few non-USM Canons (18-55mm, 50mm f1.
and the Sigma 10-20mm EX HSM.
In my experience, the fastest focussing of the lenses I own is the Canon 70-300mm L, though all the other Canon USMs are very close behind it in terms of focussing speed. The Sigma HSM is also fast, but just a bit slower than the Canon USMs imho.
Perhaps in practice I 'feel' that the 15-85mm as my current 'walk around' is a bit faster than the 28-135mm USM which I used to own till a few weeks ago. I've never tested that scientifically, and the difference would be small. I know that my Canon 100-300mm (while not so great optically wide open, particularly not at 300mm) - was able to capture some sports photos due to its focussing speed that other non-USM lenses I had tried couldn't.
I wonder if there are more aspects that come into play to actually answer the question (eg some lenses might focus quicker between smaller focus differences (eg between 10m and infinity focus) - whereas be slower from the 'macro' (MFD) to 10m range.
The theory that a prime lens should be able to focus quicker (because of the less complicated design compared to a zoom) might be true. A quick note - when I want very quick focussing (eg when I take some photos of motorsports, I nearly always switch my IS off, and I wonder if that gives me slightly quicker focus speed too.., though sometimes I have IS on - eg mode 2 for panning).
Also, I think it depends on the amount of available light. My understanding is that if there is low light (or low contrast) a lens at least f2.8 or faster will gain the focussing precision of many Canon DSLR sensor's "extra precision f2.8 cross focus point" (in the centre AF point). I've heard many people say that their 85mm f1.8 is very good at quick focus for eg indoor sports (where I could imagine eg a Canon USM lens which has f5.6 might struggle, or at least 'focus slower'.
Finally, another point while on this topic. My Canon 100mm macro (non-L) focussed quickly and accurately, also at 'non focus distances'. I often use it for portraits and subject isolation (and can use the handy focus limiter so it doesn't search / hunt near the macro range). However some people have complained about their Canon 100mm USM nonL's "slow focus speed". I've read in a few places that the later batches of some Canon 100mm USM nonLs focussed quicker. (and yes, I am aware there is a non USM Canon 100mm macro too... I'm not including that in this discussion).
For my use, my 70-300mm L does everything I want it to do, including fast focus. I mainly use it for wildlife (including birds in flight), and occasionally other moving subjects (eg motorsports, or casual sports or children camps). So I realise that's not quite as demanding as some other applications.
Hope my post is useful, even though I'm conscious I am raising some new variables into the equation!