I'll tell you what I would do; please realize that I am not a trainer or anything, I've just read a half dozen books and have a Mens Health subscription.
1) Get LEAN (6-7% bodyfat). Even if you are a weakling, having a low bodyfat % will make you look stronger. Look at Brad Pitt in Fight Club, he probably weighs 145lbs in that movie, but looks huge. That's all about low BF%. Getting down to 6-7% is a long term goal (for me anyway, you may already be there). You'll need to approach that in stages (depending on where you are now). There is an old saying that six pack abs are not made in the gym, they're made in the kitchen.
1.1) Get lean by finding out how many calories you need each day. (see here http://www.scientificpsychic.com/health/cron1.html
) and create a 500-1000 calorie deficit each day (whatever you can stomach). If you need 2000 calories each day, you can create this deficit by either eating 1500 calories or by eating 2000 calories and running off 500 calories (or any combination).
1.2) It is HARD (read: almost impossible) to get lean and get strong at the same time. I wouldn't even try it. Drop a few pounds of fat, gain a few pounds of muscle, drop a few more pounds of fat, gain a few more pounds of muscle, and so on.
2) So, to get strong all you really have to do is lift and eat. You body can put on about a pound of muscle / week. So to do this you need to lift at LEAST 2 days per week (preferably 3 days/week). Do not lift 2 days in a row as a beginner. You are a beginner for at least 2 years. AND, this is important, you must EAT an EXTRA 500 calories/day. I would eat a balanced diet of nutrient rich foods (no candy or sugar drinks). Make sure you include protein in your diet, but don't avoid carbs.
2.1) If you just want to get stronger and are not looking for any sports specific workouts. Then I would suggest the following training program.
3 sets of 6-10 reps for each exercise (select a weight that you can only lift 6 times, increase that weight by 5-10lbs once you can lift it 10 times)
Bent Over Rows
Day 1 - Workout A
Day 2 - Workout B
You should focus on doing olympic style exercises (squats, deadlifts, bench press, etc). I personally hate the bowflex or any machine for that matter. I don't think they work nearly as well as free weights or even body weight for that matter.