Living in the United Kingdom I can get quite annoyed by alphabetical lists that don't allow you to type the first few letters1. As I'm mainly active on Stack Overflow I suspect what you're suggesting would be equally annoying; though, I recognise the points raised in your comment on Assad's answer are pertinent:
The timeout between the P and H for this is far too short for people
with physical disabilities / accessibility challenges to use
effectively. Yes - a quick typist sitting with a full keyboard can
navigate on most modern browsers. Not so much on mobile and touch
interfaces that lack a full sized keyboard or see tapping the pulldown
as a reason to bring up the soft keyboard at all.
The simple fact is that the most used sites in the network are the ones people will be looking for most. It may not work well for people on mobiles looking for physics.se but the probability is that they won't be.
Ordering by site statistics (if that's what happens) is actually the simplest way to improve accessibility for the greatest number of users.
Maybe there could be an argument for having an option to change the order but there aren't that many sites and you're forcing the majority of people who want to visit Server Fault to scroll a lot.
I would be more in favour of an auto-complete box, which would address the issue of accessibility and typing speed on mobiles etc without adversely affecting those people who are looking for the most popular sites.
1. Especially since some sites decide that I live in England, Britain, Great Britain or the UK / U.K. so I'm never really certain where I'm going to find the "correct" country.