Missing Secret on level 6, The Crusher:

The secret that's usually overlooked is a Megasphere near
the level's starting point.

Look on your Automap.  Near the middle of the level is a
fairly large, square, dimly-lit room containing a small
forest of pillars which run floor to ceiling.  In the
southeast corner of this room are a pair of pillars: one is
vaguely "U"-shaped on the Automap, and one close to it
which appears as a simple square on the Automap.  Walk up
to the north face of the "square" pillar and you'll notice
some markings running in a line up the face of it.
If you Activate this pillar, as if the markings were a
switch, it drops down, revealing a Megasphere.  Grabbing
the Megasphere counts as a secret achieved.

To download a demo that shows how to access that Megasphere
on this level, click here.