Foolish Question: Can I move apps in the Applications folder?

~ Foolish question, especially for someone who fancies themselves a Mac Tech:

Is it okay to move apps that have been installed in the Applications folder into sub folders? And if I do that, will it mess up aliases in the dock? What about non drag and drop apps (like anything from the Adobe Suite), will those break the links with their libraries if I move them into sub folders?

I'd just like to be able to put them into folders for better categorizing, rather than having a huge list of icons, and the only problem with Launch Pad is you can't do folder in folder, nor can you go above a certain number of apps.

Thanks!