Are you running a ton of CPU/IO intensive jobs at the time? Do you have any Server monitoring tools that you can look back at CPU and IO usage?

How much memory is in this server and do you have SQL Server consuming all of it or are their apps installed on this server and everything is swapping memory......

Do you have a lot of IO intensive databases on this server?

Do you update stats on a regular basis, Rebuilt Indexes??? (thinking that you have long running queries that might be helped by doing these two.... a long shot)

If your data drive is more than half full have you stopped sql server and defragged that drive? (again, another long shot but if you can undertake the outage worth a try)