Are side fans worth it?

Of course they are worth it, if you need the additional airflow.

They aren't restricted in their side panel mounting either as intake or exhaust, it's more relevant as to where your GPU heat is being exhausted, inside or outside the case?

The 80mm fans are usually louder and higher pitched than the 120mm fans.

Rear exhaust is necessary, as is side intake. The difference was huge once I installed a side intake. My GPU cooled way down! Put in a side intake and you'll never regret it.

You want positive airflow. More air should be coming in then leaving.

I know it seems weird putting a fan that blows in from the side, but it blows right at the mobo and GPU. It is worth it.

I agree a side fan should blow air into the case. I would highly recommend it if you're water cooling your CPU. I noticed a 15c drop in surface temps from the heatsinks surrounding the CPU when i installed a RAM fan. I'd imagine a side intake would produce a similar effect.

Which of the two fan spots should I put it (refer to Newegg link). My GPU is pretty much smack dab in the middle of both.

Why not do both? If for whatever reason you can't I would put it on the bottom one. Unless your water cooling (custom or closed loop) then I would put it on top.

I have a mid tower, and I had to put my fan into the bottom slot on the side. I think there would have been an issue, as fans stick out at least an 1". Also, my GPU has a power cord that goes in on the side rather than opposite the back of the computer. (weird design, and really stupid)

Mine didn't have a spot for a side fan, but it had holes the right size for screws so I added one of my own. Good choice, right on top of my gpu, gpu temps are noticably lower at idle.

If you have more fans blowing in than blowing out you won't end up with dust and crap being pulled into everyplacey that there is a tiny crack or hole in the case.