1) replace the stock pump with a MJ900. (More flow and less heat)
2) replace the fixed outlet with a hydor rotating thing. (Less dead spots)
3) widen the opening from the first to the middle back chamber (helps with better flow and less noise)
4) get rid of the bioballs in Chambers (nitrate factory)
5) in chamber 1, you can easily put your heater and something media like carbon (same with in Chamber 3, although it gets less flow)
6) remove the sponge between 2-3 unless you like cleaning it weekly (nitrate factory)
7) remove the paint (razorblade) on chamber 2. Backlight with some simple PC setup. Fill chamber 2 with macro and set the light timer to night time while mainlight is off
There are some more elaborate mods, but the above are fairly inexpensive, easy and have a sizable impact. Search at nano-reef for a lot of examples.