How much memory do you have?
How full is your hard drive?
Had this problem with my old Mac Mini (in spite of 1GB of memory)
Repairing permissions helped, but the 60GB drive has only 10GB free and a lot of the wait is disk thrashing as it pages in and out.
I'll get a new Mini in September when Snow Leopard comes out.
(Never been a problem with my Macbook (2gb/160GB)