Secret 1: the wall next to the energy "tank" in Area 7, above Nerve boss can be destroyed. There is a secret powerup there which increases energy by 350.

Secret 2: the right vine-like plant enemy in Area 1, in the first screen where they spawn when backtracking from area 2 can be killed. It increases max energy by 100.

Both powerups take a rather long time to unveil by shooting (~40 seconds at maxed out level). A 100% run would obviously require getting them both.

My personal map (sorry for the lack of a legend :D) can be found here: https://drive.google.com/open?id=0BxSEz0UdUWv4X3BJd0xNcHJIcVU