I found the yellow weapon to be most useful in Stage 3, only because its multi-directional and it works great on both bosses.
Stage 4 has a part that reminds me of that one enemy back in Stage 3 of Metal Black that has that nasty habit of closing the top and bottom part of the passage on you if you don't destroy it quickly enough. Think of that times 5/6 and thats what Stage 4 is here.
Anyways, to stay in the race here --
ExedExes - 1,178,100 - Stage 4 - MAME

In other news, I finally won a copy of Mars Matrix for November, and it's on its way!