What version of SQL Server are you using, and what patch level?
Take a look at sysprocesses or sp_who2 (or sp_who3) and see what processes are using the most disk resources.
You can also make sure that SQL Server is actually the application which is causing the IO to spike. In Performance Monitor select Process from the Performance Object list. Select the IO Data Operations/sec counter, and the sqlservr from the instance list. This will show you the IO that SQL is doing. If this number isn’t about the same as the total IO number than something else is hitting the disks pretty hard.
Often this will be an anti-virus or defrag utility running on the SQL Server’s console which causing these problems.