I started with Starting Strength and as Mark Rippetoe advises, anyone new to lifting or who cannot squat 1.5x their bodyweight should stay on Starting Strength until they can. I was pretty close but wish I had stayed on it until I had.

After Starting Strength and for the majority of my "bulk" I did Layne Norton's "PHAT", which combines power and hypertrophy training (and which you can find tons of information about on this site and on simplyshredded.com, as well as google searches, of course). There are two versions, "old" and "new", and I combined/modified them to look basically as follows (and, yep, monday is leg day!):

Day 1: Lower Power

Squat (3-5 x 3)
Hack Squat (6-10 x 2) 
Leg Extensions (6-10 x 2) 
Stiff-legged Dead Lifts (5-8 x 3)
Glute Ham Raises (6-10 x 2) *
Standing Calf Raises (6-10 x 3) *
Seated Calf (6-10 x 2) *

Day 2: Upper Power (old version, basically)

Bench Press (5 x 3)
Bent Over Rows (5 x 3)
Military Press (5 x 3)
Pull-ups (6-10 x 2) 
Dips (6-8 x 2)

Day 3: Rest

Day 4: Lower Hypertrophy

Speed set: Squat (3 reps x 6 sets - at 70% of 3-5 normal rep max)
Hack (8-12 x 3) *
Leg Press (12-15 x 2)
Leg Ext (15-20 x 3)
RDL (8-12 x 3)
Lying Leg Curls (12-15 x 2) *
Seated Leg Curls (15-20 x 2) *
Donkey Calf Raises (10-15 x 4) *
Seated Calf Raises (15-20 x 3) *

Day 5: Upper Hypertrophy (modified to 1 day rather than back/shoulders chest/arms split)

Speed set (press): Flat dumbbell press (3 reps x 6 sets - 65% of normal 3-5 rep max)
Incline Dumbbell Press (8-12 x 3)
Incline Cable Flyes (15-20 x 2)
Seated Dumbbell Press (8-12 x 3)
Upright Rows (8-12 x 2)

Speed set (pull): Bent over rows (3 reps x 6 sets - 65%)
Dumbblell Rows, Seated Cable Rows, or Close-grip Pulldowns (8-12 x 2-3)
Dumbbell Concentration Curls or Preacher Curls (8-12 x 2)
Seated Tricep Extensions, Cable Pressdowns or kickbacks (8-12 x 2-3)

(*depending how I felt, sometimes additional accompanying movements, ..sometimes less)

Day 6: Rest

Day 7: Rest

* Movements routinely rotated with glute ham raises and lying/seated curls include: weighted hip thrusts and bridges, "donkey kicks" done underneath the leg curl machine or smith machine, hamstring pull backs on the smith machine, reverse hyper extensions, weighted kickbacks, and weighted step ups.

* Rotated bulgarian split squats and lunges with hack squats on hypertrophy days (and when the hack machine at my gym temporarily went out of commission I started doing them on the dreaded smith machine, feet way out in front. Not bad, if your gym doesn't have a hack machine.)

* Calf raises rotated with rotary calf extensions and extensions on the leg press machine

After Phat I did a couple cycles of 5/3/1 and then began to "cut". For cutting I for the most part followed Martin Berkan's guidelines found on leangains.com (including Intermittent Fasting with fasted training), the philosophy being to hit it hard but keep it simple while in a caloric deficit in order to maintain as much muscle as possible and not tax the CNS, which makes sense. He recommends no more than 5 movements per workout, 3 days per week, following a "reverse pyramid" scheme. This is (basically) what I did:

Each movement 5-7 reps, 2-3 sets, 3-5 minute rests

Day 1:
Squats 
Leg Press (with a set or two of calf extensions while I'm there)
Walking or Barbell Lunges, Bulgarian Split Squats, or weighted Step-ups
Overhead Press
Chin-ups

Day 2:
Bench Press
Barbell Rows
Pull-ups
Dips
Jump squats (3 sets, 20 reps)

Day 3:
Deadlifts
Leg Extensions
Weighted bridges or hip thrusts
Kickbacks, donkey kicks (on smith machine or under leg curl machine), or glute ham raises
Planks (3 x 1:00)

I also recently added in 50 bodyweight squats per day, everyday (which I totally stole from chickentuna), and I don't do cardio (though sometimes I'll jump on a stairmaster, just cuz). I do yoga 3 or more times per week but I do this mostly to stay loose, limber, and sane rather than anything else (along with the 5 tibetan rites every morning for the same reasons). I often dance 1-2x/week (just cuz), do planks and push-ups whenever the mood calls me (usually commercials during football games), and that's about it. Not sure what I'm going to do next for maintenance but I'm sure it will look much like the above.