The Basic Concept:
Effects, Tools, and sub-Tools are all related but different.  Explaining them is a little tricky, but in most instances it doesn't really matter if you know what they are.  Generally speaking, here's the basic idea:  the Effect is what you want to do and the Tool is how you do it.  But some Tools require sub-Tools to do the real work.  For example if you have a character that you want to deform with bones, you'll choose the Bone Deform effect.  That effect uses a Skeleton as its tool (just like in real life), and that skeleton will be made up of Bones (also like in real life).  

But Sometimes...
To slightly complicate it, there might be times when you use a Tool (and maybe its sub-Tools) without the Effect it was originally intended for.  For example, you might use the Curve tool and its sub-Tool, Points, which are normally used with Flex or FlexMotion) with bones, parenting the bones to the points on the Curve (the curve's sub-Tools) and using the points to move the bones.

And Other Times...
Some Tools exist independently of any Effect, such as Cameras, Lights, Nulls, and Procedurals (though the Light Tool does have sub-Tools, which are the lights themselves; see the table below).  There are some Effects that use Nulls as their Tools, but there are lots of times when you'll use Nulls without effects.  For example, you might parent your character and all of its IK goals to a Null so you can position it in the scene easier.

Sub-Tools:
Sub-Tools can not exist without a Tool.  In other words, you can not have a bone unless you have a Skeleton.

The List:
The following is a list of the current Effects, Tools and their related sub-Tools: