That could be a lot of things from hardware, application problems, to resource exhaustion.
Previous poster said to open up Activity Monitor and look for the resources being used and page outs. You didn't say what OS you were using. Even Leopard can push 1G to its limits.
Here are some some things to look out for in the system:
1. Running out of free drive space. If this is true and your swapping, swapping would take excessively long. Like the previous poster implied this will tell you if you have too little memory. At least 10% of your drive should be empty.
2. For some reason Spotlight is continually indexing. This can be checked by clicking on the Spotlight indicator in the upper right corner and seeing if it's active. Also, in Activity Monitor, organize by name and search for mds and mdworker threads being active. This can happen if the indices in Spotlight get corrupted. In Tiger and Leopard, the system seems to like to do a full re-index at the drop of a hat which is time consuming and will definitely slow the system down. It seemed it was fixed in Snow Leopard and Lion, but now it seems like it's a problem again in Mountain Lion. If this is the problem, you could move ALL drives into the privacy section of Spotlight, which will prevent it from running, but you also won't be able to use Spotlight, since it won't search for anything.
Possible hardware problems:
1. The drive has problems. Although you said Apple tested it, they're drive testing tools are pretty Mickey Mouse if you ask me. I've seen Scannerz listed on this site a few times and it can pick stuff up like failing but readable sectors. This is a possibility, but I doubt it. You didn't say you had any read or write problems where a dialog comes up saying "Can't read/write to drive" or "I/O Error" so I wouldn't automatically assume the drive is a problem. In other words don't rush out and throw 30 bucks or whatever at Scannerz because that's probably not your problem.
2. Your heat sink has come loose. It happens, not a lot, but it happens. If this has occurred the kernel will likely a) kick on the fans in high speed, and b)throttle the CPU speed to a lower speed to cut power consumption. On BSD systems this will show up in the log files in /var/log but I don't know it it shows up at all in Apples. It might be worth checking.
My personal guesses would be too little memory combined with too much drive space usage resulting in tons of slow swap outs, or GOOD 'OL SPOTLIGHT being a warthog, yet again. These are educated guesses so please keep that in mind when reading this.