Now that I've been able to lose most of the body fat I possibly can (standing at 9-11 percent depending on the day), I now want to gain lean body mass, i.e. muscle mass.

For some reason gaining muscle in my legs is fairly easy (biking might be helping). It give me a happy "problem": I have a hard time pants that fit me since pants I would be comfortable in are too baggy on the waist. I even outgrew a pair of shorts a few years ago because my legs had become too muscular.

But the upper body seems to be more problematic. No matter what kind of exercises I do (3*6 for 3 weeks, and then 3*10) I never seem to pack more muscle above my waist.

Is it the way I exercise or the way I eat? I've always been told that one can safely eat one gram of protein per pound of body weight so I should be eating around 170 grams a day. I'm probably under that amount - being an intern can be expensive - but I would wager I'm above 100 grams.

What about exercises? Are there 1-hour routines that could help me pack more muscle?

Give it time.
No magic potion.
No magical exercise.
Muscle mass takes times to gain. As long as you are steady with it, you'll gain it.

I'm sure you already know, but high weight, low reps (8 or so) are going to build mass the most.

Also, maybe try only 2 sets instead of 3 on each muscle group. In fact, SOME muscle-heads even do only 1 set of each muscle group (after a warm up) and push their muscles to their limit in one set only. There risk on injury is a little higher that way, so I would recommend 2 sets. And make sure that at the end of each set you push you muscle to fatigue.

Food? Lots of protein, obviously. Eggs, chicken, fish, tofu, protein powder are all good sources. Water is important too, it helps your body have the right chemical environment to build protein fibers in your muscle cells.

Light Knight : Protein is *usually* not a problem. I'm on an internship so my means are a little more limited, but I easily get over 100-120 grams when I do muscle training (I eat a dozen eggs on such days). I also eat half a pound of (regular) ground beef and half a cup of sunflower seeds.

Pushing myself to fatigue is usually not a problem except for legs. I seem to have some balance issue and fell a few times, hurting my lower back and ankles. However, I seem to be unable to get past some plateaus; I've never been able to lift more than 50 pounds with dumbbell shoulder press. Dumbbell chest press also gets pretty hard as I can't get the "initial" push on my own without help.

I disagree that high weight and low reps is the best way to gain strength. That is an old school thought process and really the whole thing depends on where you are fitness wise.

The thing is that you want your muscles under tension for the longest period of time. So usually especially when starting out, lower weight and high reps will give you the lean look you are looking for.

http://www.bodybuilding.com/fun/high-reps-low-reps-which-rep-scheme-is-best.html

Then you need to focus on Nutrition. Protein needs to be a high focus here. Especially post workout.

Any sort of high protein per serving and low carb Whey Protein powder/drink will do the trick. Most people think they are getting enough protein in their diet, but they are not http://www.bodybuilding.com/fun/maki1.htm

The amount of Eggs and Red meat you are eating could cause you issues with your cholesterol. I would suggest finding leaner forms of protein like Chicken, Pork, and Turkey. Beans and such are a good source as well on top of the Protein supplement that every person trying to make gains should be taking.

I think I figured it out: avoid routine. I do the same exercises for 6-8 weeks but change the # of reps after 2 weeks. It seems to have been efficient as I gained body mass while still "floating" in my shorts.

As for the food: dietary cholesterol has generally a low influence on LDL. What shoots it is generally trans fats and too much carb - so I avoid beans.

janus : I'm not sure why you would be avoiding beans. Beans are one of the best and cleanest forms of protein and depending on the type of bean you are talking about are something you should really be getting into your diet. Much more so than any type of red meat.

http://www.webmd.com/diet/beans-protein-rich-superfoods

With regards to your workouts. It's always best to change up the exercises you are doing and the weight in which you are using. Changing up the reps and the sets does provide some benefit, but less so than just targeting muscles in a different way by changing up the exercises you do.

That's the problem: beans are recommended based on the faulty assumptions about red meat. It is NOT bad for your health (unless it's stuffed with corn) and is much more filling. Most legumes are 50% starch, i.e. simple carbs linked by weak bonds.

As for muscle training: I have a day for every muscle group so I pretty much exercise all angles. I vary reps every few weeks to change how the muscle exercises

Have you tried doing push-ups and sit-ups? When I was going through Basic Training, I was nothing but a twig at 150 lbs. Then, when I got out, I was literally 175 lbs of muscle about 9 and a half weeks later. 

janus : I was 115 kg ......after 6 month gym and diet my weight was 81 kg......after 1 year gym now my wight is 87 kg....I go in gym 4 days per week.......1 day chest/biceps 2 day back/triceps 3 day legs / shoulders 4 day biceps/triceps.......I gain for 6 month 87 kg-81 kg= 6 kg