File resolution, how to crop and preserve clarity?

Hello, I record video off my PC using FRAPS, copy it to my mac, and cut out the clips I want using Quicktime pro 7. The problem I run into is when I import them into FCE they are resized improperly and become fuzzy. I realize FCE is a "Fixed Resolution App" (Glares at Apple). How do I import the video keeping the same resolution, but only cropping the video. I know I lose some quality converting from AVI to MOV but that is nowhere near the loss of quality once it is resized by imovie/FCE.
it should also be noted, the LCD I use is native 1280x1024, I record in "50%" mode, hence the 640x512 output from FRAPS. So simply adjusting my monitor to 1440x960 won't work. Also I realize I can do all my editing/compiling in QT7, but seriously, that's not a solution
Any suggestions?
Thanks in advance!
example:
http://www.sonic84.com/tmp/comparison.png
left: original: 640x512
Mid: FCE: 720x480
Right: iMovieHD: 720x480

The standard definition dimensions of video are 720x480 using CC601 pixels with an aspect ratio of 0.9. How would you like your video to fit into that frame? It can either scale down and you'll have pillarboxing, or it can scale up and crop. Scaling up is never a good solution. Furthermore, I'm guessing you're talking about screen captures, which probably are in resolutions much higher than can be compressed well into a highly compressed format like DV.

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