How to do a clean reinstall of everything

When I got my new MBP, I did the migration assistant from my PMG5. One or more of the programs were PPC OS9. After migration, I noticed the MBP ran very slowly and had strange Icons in the title space of the folders.
I continued on, loading bootcamp/XP, parallels, and lots of software. When my CAD began acting very slowly and crashing because of out of memory (in 2GB RAM), I new it was time to clean everything off and start over. The prospect is daunting.
In preparaton, I have made dmgs of my Mac HD and the Windows partition on an external drive. One thing I am afraid of is loosing all my emails.
Can anyone give me a cookbook way of going about this?
Thanks
Mini(CD2), Imac(CD2), G5 PM, MBP(C2D2.33, 2GB)   Mac OS X (10.4.9)  

-g
Thanks for the comments. Let me clarify some of my comments.
When my CAD crashes, it is only the program, not the Mac. It crashes because it uses up the memory during rendering and does not release it back, finally running out of memory (2GB). I don't know where this fault lies, I have told the CAD company.
When I first got the MBP, I used Migration Assistant to transfer all the files from my G5PM to the MBP. All this is detailed in another post by me. <Re: New MacBook Pro App Migration results in strange icons>
All of a sudden an icon came out of nowhere to reside in the headers of folders. I traced it to PS7 "PPC accelerator" in some library, which I deleted. Now there is a "?" in the folder header instead of the previous icon. I have since deleted PS 7 (I think), but the "?" is still there.
I should have started all over earlier, I just didn't notice it soon enough.
Now, the computer is very sluggish at times, taking 1-2minutes to boot. Sometimes taking 1 minute to load SeaMonkey (8 sec is the fastest time).
When I showed the machine to a Mac Tek, he recommended I wipe it clean and start over. I have no intention of reloading PS 7.
So, that brings me to this thread. How to do a full install the easiest way.
You said to back up my mail folders. I haven't seen a way to do that. SeaMonkey is my browser/email app.
Mini(CD2), Imac(CD2), G5 PM, MBP Mac OS X (10.4.9)
Mini(CD2), Imac(CD2), G5 PM Mac OS X (10.4.8)
Mini(CD2), Imac(CD2), G5 PM Mac OS X (10.4.8)

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