Your guitar routine should depend on your style of playing, level and on the amount of time you've got to play guitar. Check out Steve Vai's 30hr guitar workout. It's a bit extreme but has some awesome ideas in there.
Decide on what type of guitar player you want to be. That will tell you the areas you want to work on. If you want to be a metal player, concentrate on picking technique, muting etc. If you want to play jazz, work on music theory - stuff like chord-scale relationship, understanding harmony(this will take you a few years).
Choose 3-4 techniques and work on them 1 technique a day. For example, I'm a rock player inclined towards improvisation. Here's what I try to work on:
Mon & Thu: Alternate Picking
Tue & Fri: Legato/Tapping
Wed & Sat: Economy/Sweep Picking
Sun: Music Theory
Now, I try to work on 3 things each session -
Warmup - very IMPORTANT. You're going to feel like shit if you jump into the exercises directly. 10 mins of this should be enough.
Exercises - Pickup exercises from books/magazines/videos and work on them. Try doing all of them in the same key. Its pointless doing an exercise if you can't do it in a musical context. @bluevoodoo1's post talks in depth about this.
Jam - Play over chords/backing tracks/with a friend and use only the technique you've decided to work on for the day. This is my favorite part of the routine and IMO the most helpful. Try to spend equal time on exercises and jamming.
Have a day off every week. Use it to read up on music theory or to write new music. Be creative.
Remember, this is a mere guideline. Try to be consistent but make sure you don't burnout by changing things around regularly. Take a day off once in a while to learn a new song or just jam. Any routine is pointless if you're not having fun doing it.
I hope this helps.