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Anything that runs at a system level (Today plugins, HackMaster, etc) and anything that gets used regularly (Pocket Informant and TomTom amongst others) get installed to Main Memory - where access is fastest.
Infrequently used apps get installed to the SD card that lives permanently in my 3970.
Big data files (GPS maps, MP3s and videos) go on the 1GB CF card.
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