That paper, like most papers on timing attacks, was done on the local network, not the internet. They're relying on absurdly precise measurements of absolutely tiny differences in timing, which would be lost in the jitter and latency of the real internet.
As I said, you can certainly do internet timing attacks where you're looking for database access, because this can take many milliseconds, which is a delay which can be detected even on a crappy internet link using a bit of light statistics.
Even if I'm misunderstanding, though, this particular remote timing attack is probably not practical in most programming environments; (for instance) straight C memcmp is below the measurement floor, even with signal processing.
That is a great paper; also, check out Crosby and Wallach for the modernized, math-ier take; with signal processing, the measurement limits are nanoseconds on a switched LAN (ie, if you could get a box deployed in the same hosting center as Blizzard) and tens of milliseconds over the Internet:
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.65.9...
... and Nate Lawson's Black Hat talk which actually goes through the practical issues trying to set up and run these attacks against real systems:
http://www.youtube.com/watch?v=ykNt8pSQFZQ
It's very modern, as you describe, with all the fancy maths and all that.