This is always a big topic of discussion. While I am no professional, I feel a have a pretty good grasp on this. Anyone feel free to add on or challenge.
ISO Adjusts your sensor's sensitivity to light. Lower it for more detail and when you have plenty of light. Raise it as your light source gets dimmer.
Shutter Speed How long your shutter is open allowing your sensor to be exposed to more or less light.
I know a lot or all of anyone reading this has read a book or about this somewhere else. The best thing I can suggest is, instead of going around shooting, pick a time of day. Choose 1 subject, flip over to M, look at your settings, take a picture. Make adjustments to ISO only, take a picture. What happened?
Ok, leave your ISO alone (bright day light flip it back to 100 or your lowest setting). Go to your f/stop. Lower it all the way (2.8 etc.). Your lowest f/stop is considered "wide open".
Seeing a trend here? Change one setting at a time, at the same shooting location at the same time. Look at what's happening to your shots. Practice, practice, practice. Make a conscious effort to focus what you've read in your books in to practice.
I really don't know how to explain how it "clicked" for me. Practice and paying attention to what was happening. I did just what I said earlier. I sat down and took about 50 shots of just one thing making changes one at a time. Went to the computer looked at the EXIF data. Read a lot, learned how to read a histogram, how to read the exposure reading on the camera. The +_|_|_0_|_|_- readout.
I hope this didn't make things more confusing for anyone and helped someone.
UPDATE: Meet Aperture. To get this thread flowing let's discuss what else we see different (not just the picture but description) besides the shutter.
F/5 ISO 100 1/200
F/10 ISO 100 1/200
F/25 ISO 200 1/400