Scenario #1: Tracking speed progress
This is probably the most common use and is most likely the first thing that comes to mind when you think of practicing with a metronome. You would choose a riff or exercise to work on, start slow, and then gradually increase your speed on the metronome. The key here is to have patience and be honest with yourself so you do not increase the speed before you are ready. You should only increase the speed when the excerpt you are working on begins to feel effortless. And remember to always record your progress in a notebook of some sort.
Scenario #2: Developing a good sense of rhythm
This one may be fairly obvious as well, but good rhythm is probably the most important asset for any musician, especially if you want to play with other musicians. The metronome is invaluable for developing flawless rhythm. One of the best routines you can do for this is to play familiar music at different tempos. First choose a song, riff, or whatever that is familiar to you and that you can play fairly easily. Play through at the intended tempo, and then bump up the tempo 10 clicks each time you play through it until you are struggling to play it. Once it is out of your range of speed, go back to the original tempo and this time move the metronome down 10 clicks each time you play through it. You'll be amazed at how difficult it is to play something accurately at super slow speeds.
Scenario #3: Subdividing the beat
Subdividing the beat can be fairly difficult to comprehend for some, so I will do my best to simplify it as much as possible. Start with your metronome at 60 beats per minute. Each beat will represent a quarter note. In order to subdivide the beat, we have to divide the value of one beat into two equal beats which means the tempo will feel twice as fast. In reality the tempo is not what has changed. We have simply moved from playing quarter notes to eighth notes. What I recommend here is to play quarter notes at a medium paced speed, 80bpm for example, and practice subdividing the beat in two ways. First, practice getting a feel for moving from quarter notes to eighth notes. You can always check your accuracy by doubling the speed of the metronome (quarter notes at 80bpm becomes eighth notes at 160bpm). Second, practice going from quarter notes to half notes. Play one note for every two beats of the metronome. This will make you feel like you are playing at half speed. Once you get a feel for the basics you can move into sixteenth notes, triplets and beyond. Being able to subdivide the beat is crucial for counting and playing more complex rhythms.
Scenario #4: Learning music by ear
Incorporating a regular and consistent metronome routine into your guitar practice not only develops your chops, but it also develops your ear. Hearing and matching pitch is only half the battle. Once you master the metronome, you will be able to hear and repeat a rhythm with greater ease and accuracy. And just like everything else, the more time you put in, the greater the reward. In this case, being able to hear a song and play it back after hearing it only once.