As your hard drive fills up with data, it takes longer for it to seek to find free space for data that needs to be written to the drive.  Also it takes longer for it to read out the data because it has to go through all that data already written out to the drive to find what it is looking for.  I once tried to update a windows box by using the in place upgrade function.  Wrong move...it slowed to a crawl.  Besides it left behind a windows.old file on it where everything from the old install was kept and took up a huge amount of space.  I ended up backing everything up and reinstalling windows.