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Glad you started this, as I've been wanting to ask the same question.
I've been using FRAPS to record gameplay footage for OTHER games, but it doesn't seem to want to work for RPG Maker. I suspect the engine is grabbing the key presses and not passing them through to FRAPS, and FRAPS also doesn't appear to have a "record this section of the screen" option, but only records the active window.
Camtasia Studio is really nice to use, especially for editing, but it's not a free product - there's a 30 day trial, but to buy it's several hundred dollars.
There's a watered down (free) version - CamStudio that I used to use that doesn't have as wide a range of functionality. I've been meaning to grab it again and see if it works with RM.