A couple of slightly off-the-wall causes I have seen before:

- The network guys had made a change to firewall configuration / internal tcp/ip routing which was noticably slowing down the traffic. (They wouldn't tell me precisely what they did, I think they were embarassed cos they initially blamed the applications for causing the problem and I spent a week proving otherwise)

- On one occasion the hard drive of a server was 99% full (mainly due to the guys keeping several months worth of old backup files). Made everything crawl on the server. It was so obvious a problem that no one had thought to check.