System.gc() considered harmful
I recommend that glassfish have the switch to disable explicit garbage collection with System.gc() included in the default installed setup. I inherited code with an explicit gc() call, and I suspect a 3rd party library was also calling it.
This blog entry sums it up nicely: http://java-n-stuff.blogspot.com/2009/08/turn-on-disableexplicitgc-now.html
With this and some other performance tuning glassfish is running much better for me.