Format or not to format.

[Zealord]

Well, recently, I haven't formatted in about a year's time

You mean defragmentation? As formatting does not really do any good. And no, after a year your disk won't be as extremely fragmented to cause the problems you have.

I've had to turn down to high, some low settings, going below 50, but avg 60. It could be my CPU, I could overclock it, atm it's a i5 750 at stock, 2.66ghz, but I'm not sure.

No need to over clock. Install speedfan and check if your stuff is overheating. If so, clean/replace fans and component paste.

Also; in some games, in darker areas, I've been getting faint grey-ish black lines across my screen, hardly noticeable, but you know, they're there, and it bothers me.

Turn Vsync on (Not recommended, eats a lot of memory) and check your graphics card driver software for extra options.

Now, Black Ops 2, I run it maxed out everything on, highest, w/e, I'm getting stuttering issues, freezing issues, lag, everything, but I get 150-200 FPS, never below 85.

Try running on all lowest graphics and see if it persists. If it's not the case, try upping/downing each setting individually to see what causes it.

Maybe my HDD is just clustered, obviously it's not a bottleneck by my CPU, as it wouldn't cause that, would it?

How can a HDD bottleneck a CPU to such extreme extents?