I play this game a lot. And through frequency of playing it, I've descovered secrets that I haven't seen anywhere else on the 'net!
The 3rd Level Charged Shot
When your life meter meter is flashing red, (so you only have 2 slots left) you can charge up past the 2nd level. You still flash yellow, but if you hold it in a while past when you start to flash yellow, you'll let loose a HUGE blast that does tremendous damage!
I've also managed to get some screenshots of it in action.
I'm not exactly sure how to get this one to work. I think it has something to do with the majority of damage going to the top of the first phase of Wily's mech. Basically, instead of turning into the flying thing with the wheels and lightning, it tuns into the bottom half, the UFO thing.
I've got 4 screenshots of it.