Uncle 111 has finished archiving transcripts from season 3. If you are interested in taking a look, pop on over.
Also, there is a sister site set with archived information as well. Note that the address is Zephyr Ave. Sydney's street address. Clever!
PS. In related news, my sister recieved a copy of the Alias pilot script from eBay yesterday. It's just a Xeroxed copy of the original with the copied signatures of Merrin Dungey (Francie), Bradley Cooper (Will), Kevin Weisman (Marshall) and Greg Grunberg (Weiss) from those of the signatures I can read. I was flipping through it and noticed a lot of lines were changed. Once I can actually sit down and look at the whole thing, I will give you a mini-report on the differences.