There are several common ways to indicate that a GUI label is clickable:
Set hyperlink style (underline and blue) Cons: this steals attention and becomes a distraction for those familiar with a program.
Grey-out inactive elements. Works for checkboxes, but isn't suitable for text.
Add tooltips - user will hover over elements and learn what is clickable. Cons: user still might miss an element and the upfront cost (creating tooltips for all elements) is high.
Change background of all active elements if a hotkey is pressed. Cons: user must be fairly familiar with the program in order to know about this hotkey.
Show tutorial (similar to one on Stackexchange). Works for introduction of basic concepts. Cons: tutorial can only show most important functions because a user wouldn't watch a lengthy video. Besides it doesn't help when user is working with a program.
What is the most intuitive and non-invasive way to present active elements?