Modding my case by adding a side panel window.

I want to be able to see all of my motherboard. I don't want to see the drive bays, so it will stop there. Thanks for the sites!

yeah, a 12X12 sheet will do fine. They are around $10 from mnpctech. You can always cut it down.
Most people don't want to see their drive bays. I kinda like full windows right now. But a 12X12 will allow viewing of only the parts you want to highlight. So cable management is easier, not necessary to hide as much.

If you don't care to cut your own fan hole, you can order precut ones from www.frozencpu.com. However they are much pricier.

Where exactly should I put the fan at?

Typically blowing fresh air on your graphics card is ideal.

But wouldn't that negate putting a window in? If I put a window in, and then put a fan in the middle, won't it take away from the effect? Wait, I have an idea...what if I do a big jagged circle with tendrils reaching towards the middle of the circle, where a 140mm circle is at. Then, put a Scull fan guard there, and install a 120mm fan behind it, so it is hidden?

*Skull

Yes those are good ideas. If you don't wish to have a fan there, you could just put some holes or some other venting. Or none at all. You already have a fan positioned there, but its not necessary to have one in your side panel. Depends on how hot your GPU gets.

Its entirely up to you of course. I admit if showing off your motherboard is your goal, a big honking fan in the way would not be desirable. In fact the 120mm fan on my Antec 900 is a bit too high for my tastes and I've had to modify the case to accept some rather large heatsinks. It actually blows on the back of the card a bit but mostly toward the motherboard. Due to my mobo config, I had to use a lower PCI express slot.
Consider just putting a window in, since it will be a small window. You could always decide to put a fan in later.
I would not recommend the molding style windows, they are a bitch and a half to get in. The method demonstrated by mnpctech with the tape of the gods is easiest and the results are nice. However I would leave the edge of the window cut a little rough, I had some trouble with the u channel popping out. I also recommend a bit of glue to hold the u channel in place.

Or a bolt on may appeal if you like that look. You just have to leave a half inch or so beyond the cut for drilling holes in the window, then mounting.

I was going to use a 0/16in. polycarbonate sheet and place it behind the cut out window, as my hole is going to be irregular. Since it isn't very thick, I should have no problem. I was going to use silicon glue, but is that a good way to stick it together?

I suppose its possible. But if you use that 3m tape it is very strong and you don't need much to put your window in. Watch the video on mnpctech where they install a computer on a window using nothing but that tape.

it won't let me post a picture to show you what it will kinda be like

That's what the circle will look like, but I am gonna take the skull out, make a smaller 140mm circle, which will then house my fan guard, shown here:

http://www.crazypc.com/products/CPC8011CH.html

Hopefully, I can find one that is 120mm, or I could drop the circle down to 100mm, and use a 80mm fan instead

Best answer selected by Coastaltuba.