Custom water-cooling is where you get each component (pump, radiator, CPU block, reservoir) seperately, assemble it yourself and fill it up.
A CLC (Closed Loop Cooler) is where you receive it assembled and filled, and all you do is just mount it to the case and CPU.
Benefits of custom water-cooling is that it performs far better than CLC options (which perform like mid to high end air coolers), with greater flexibility as you can pick any part you want and can include things like the graphics card to the loop if you wanted. Downside is that its quite complicated in both choosing the parts and assembly, and costs a fair deal.
Which is where CLC options come in, their simple to install since its all done for you and cost less (though for the price of a H100i, a custom kit isn't too far off price wise). Though with CLC coolers, what you get is what you get, you cant expand on the loop or customize it in any way.
If your interested in water-cooling, I suggest reading through this sticky. It will explain a lot about water-cooling and will give you an idea of what your doing.
http://www.tomshardware.com/forum/277130-29-read-first-watercooling-sticky
There is a dedicated section to CLC coolers as well.