I have wine installed on my system, although I never ever use it for anything, but in the past I did and I installed some things and now it doesn't even work well cause the wine "hard drive" located at ~/.wine/drive_c is really sloppy and ugly and I can't install many things because I also abused wine tricks a lot.
Anyway, what I want to do is just delete the drive completely, it has some big programs installed on it, and its just taking up space on my data partition where I don't want to have applications installed anyway.
However, I looked around to make sure I wouldn't be deleting anything important, and I noticed that there are some symlinks to ~/Documents and ~/Videos and even a symlink to ~/ in there.
So, my question is, if I issue the command "rm -r ~/.wine/drive_c" is rm going to recursively look in those symlinks and delete everything in ~/Documents and ~/ (all my important files)? Obviously that would be a bad thing.

I would just expect it to remove the symlinks only, but I remember reading something in the busybox configuration that there was a busybox option that would allow rm to behave that way (remove symlinks) but that it would break some standard.
I am not using busybox on my system, I am using the distro provided GNU coreutils, so I am a little scared about what might happen.

I've done this many times, just rm -fr and get rid of it all. In my experience nothing outside of drive_c was touched.

Also, remember that you can have several distinct WINEPREFIX locations on your system and all of them will contain an independent (from the others) "C:" drive.
Read more here.