System Slows Down and Freezes a LOT - Memory?  Swap?  Hard Drive?  AV?

I have a 2.4 GHz 24" dual core iMac (identifier: 7,1). It worked fine for a good while and lately I've been having problems that seem to be getting worse (sometimes it seems to get better, then worse again). I have 4 GB of memory and I'm waiting for more RAM to upgrade it to 6 GB, since I hear that's the max anyone's run successfully in this model.
I've often had a number of programs running at once. Usually I have Firefox, Apple Mail, the KDE's Konsole and Kate (from MacPorts), Calendar, Stickies, MacIago, and Pysol running. (Yes, it helps to have a few games up for breaks when I'm working.) I know that's a lot, but for well over a year, I was working with that setup without problems, without getting stuck for long times with the pinwheel of death or anything like that.
I'm not exactly sure when it started, but now I have times where I will do something and the program will freeze and I get the pinwheel of death. I wait and after 30-60 seconds I can do something, but sometimes I still get hesitations and a start-freeze&stop-go mode for a bit. Sometimes this freezes the whole computer for up to 30-60 seconds and I can't even check another space with Command-Arrow.
I've been trying to backtrack to see if I could figure out what is causing this. Sometimes killing Firefox helps, so I switched to Chrome and watched for usage on Activity Monitor and Chrome uses FAR less CPU time. I have FlashBlock and AdBlocker Plus on Chrome (had it on Firefox, and before that, used NoScript for blocking). But I've seen this happen even without a browser open.
I suspect this could be an issue with swap, since recently I was watching and saw spikes in disk usage around these times, but I'm not sure of the correlation yet. Sometimes it seems like whenever I switch to a different program, whenever I use a new feature, I have to wait (as if it's loading library code or something).
Again, this is a recent issue.
I've upgraded from 10.6.5 to 10.6.6, so I don't know if that could effect this.
I've also started using the free version of Sophos Anti-Virus (which is apparently impossible to quit once it's running) and thought it might be doing scans.
What's also puzzled me is seeing that, with 4 GB of memory, Activity Monitor continually shows 1 GB free, but still indicates 2 GB swap files. So is there a reason 25% of my RAM is not being used?
I've also checked and found my drive to be heavily fragmented. I bought iDefrag, but it can't defrag it because there seem to be some bad blocks. Rather than mark them as bad every time it hits that spot, it just tells me it can't access that part of the drive.
My guess is that OS X, for some reason, leaves a set amount of memory free to use for various reasons and that, due to fragmentation, what was once an easy task of accessing something in a swap file is now time-consuming.
Is that on target? What else could be causing this problem? This is beginning to make my iMac unusable. If it's just swap file issues and defrag problems, I'm thinking of cloning my internal 320 GB drive to a 1 TB drive and replacing the original, then running iDefrag for good measure and continuing from there. (It seems like in OS X finding bad blocks is difficult, from what I've seen.)
What can I do and does anyone have any idea what the problem is? I'll be glad to give more details if that helps, but I've tried to include as much as I can already.
Thanks for any ideas or help.

Considering how I've solved this, I'm pretty much shocked that nobody had any answers for this.
I upgraded my drive from the standard 320 GB drive (which had about 79 GB free on it). I used Carbon Copy Clone to copy my system drive to a 1 TB drive, then swapped out the 320 GB for the 1 TB. When I booted it up and started working, I noticed it was back to the way things used to be: I could go from one program to another to another with NO problem at all. No pinwheels of death and I even added a few more more running programs and still had no issue.
I have no idea why, but before, even when there was a 2 GB swap file, 1 GB (out of 4 GB) of RAM was always unused. I don't know if the OS looks at what it can access and figures read/write times and uses that to figure out how much memory it can effectively handle or what, but now I'm using almost all of my 4 GB of RAM and the swap file is smaller than it was.
So upgrading to a larger drive made a HUGE difference. I'm willing to bet that defragging the old one would have made a difference as well, but there were problems with some files and iDefrag could not read them, which also makes me suspect that drive was on its last legs and close to failure. (That and bad sectors could also have slowed down swap, along with fragmentation issues.)
The solution was a bigger drive, but I suspect defragging the old drive might have helped (if it weren't for possible bad blocks). I know deleting files from the old drive did not help too much.

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    Message was edited by: davelovesmac

    Kenichi Watanabe wrote:
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