Sudden performance decrease in SQL Server
Sounds like your statistics are getting out of date, then eventually SQL's auto update statistics will kick in and update the stats, proper execution plans are being generated, then everything starts running faster again.

If you have installed Service Pack 1 for SQL Server 2008 R2 then you can turn on Trace Flag 2371 which will change the algorithm which is used from the static 20%+500 to a changing value depending on the number of rows in the table.

If you don't have service pack 1 installed then I'd recommend setting up a job that runs UPDATE STATISTICS for all your tables weekly or nightly.