I assume that you are running Windows. It seems that the operating system (at least Windows XP) has a tendency to quickly change a working Java application when it is minimized. Bringing back applications has a kind of "lethargy."
To prevent this behavior, a fix was implemented in Eclipse. You can read about this in error 85072 . I do not think you can change that.
One question: when your system starts to hang, all physical memory has disappeared, and the whole system slows down or just Eclipse? In the latter case, GC can slow down Eclipse, so if you have free memory, you can try adding more memory for Eclipse (increasing the -Xmx value in the eclipse.ini file).
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