http://forum.ppcgeeks.com/showthread.php?t=24552
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Installing apps in the 256 program store vs Memory card will not change your available program memory. If a program needs to run at startup it will do so, irrespective of where you install it. So in a way the number of apps installed is important, but only if they rely on a process or startup program that loads in the limited 64meg memory to run the OS and apps.
Hope that helps.