Specific Exercise Recommendations
As a beginner (and I include myself in this category), you want to have a few heavy movements because you need to develop overall strength before you move on to specific body parts. This is another mistake that I made - looking at the people who already have the body type you are trying to achieve and copying what they currently do. The guys who are already big and lean will most likely be working on specific muscle groups and doing many different exercises. This is the opposite of what you want to do when starting out. The big guys built their mass and strength from doing big, heavy exercises like squats, bench press and dead lifts. Once they built the neuronal and muscular tissue from these demanding compound exercises, they can move on to work on specific muscle groups and do smaller isolation work like bicep curls, calf work, forearm work etc.
You can see some guidelines for whether you are a beginner or advanced lifter here:
(Figures are in pounds and are for 1 Rep). Alternatively, you can use the following as a rough guide for when you are strong enough to move on to isolation work:
Squat = 2 x bodyweight
Deadlift = 2.5 x bodyweight
Benchpress = 1.5 x bodyweight
Chinups = 1.5 x bodyweight (i.e. weighted chins)
Until you reach those kind of numbers, you will be far better served by making the compound lifts the foundation of your workout. Thus, I'm a big believer in somethin akin to "Starting Strength", a program developed by a power lifter by the name of Mark Rippetoe. You can find the details in the "Health Links" to the right. There are many similar variations of this program, but the general approach is the same: Squat, Dead lift, Bench press, Standing Press, Bent-Over Row form the foundations. Once these are making good progress, you can add a couple of accessory exercises like chin ups and dips.
There is NO isolation work, such as bicep curls or triceps extensions. These small exercises will not help anyone except advanced lifters. You want to be in the gym no more than every other day for about 1 hour each time. During each session, you will typically do three core exercises, for example Squat, Bench press and Dead lift. Each set will consist of two warm up sets of 10 reps, with low weight (25% max, then 50% max). Then three working sets of 5 reps. Rest for 3 minutes between sets. Keep a log of the weight and try to increase it every session in small increments.
I strongly recommend free weights for everyone as they stimulate the nervous system and accessory muscle groups so much better, but if your gym is such that you feel uncomfortable in the free weight area, then try to use the machines that simulate these core exercises until you are comfortable enough to use free weights.
As for aerobic exercise - I've outlined my thoughts on this in a previous post, but I have found that thinking of aerobic exercise as a workout for the heart and lungs instead of a "fat burner" or "calorie burner" is much more accurate. It's good for you, but don't expect it to be very rewarding if your primary goal is fat loss. The primary driver of fat loss (through caloric deficit) is the diet. It's so much easier to eat 500 calories per day less than it is to burn an extra 500 calories per day through exercise. We all know how slowly the calories tick up on the treadmill if you put it in calorie mode...
I finally got lean when I realised it was my diet that was the key and achieved a fairly low level of body fat without the torture of an hour on the running machine every day.
Lastly, a word about "toning" and another myth of the diet world - you do not get "toned" by doing high reps and "big" from doing low reps. You get "toned" by stressing your muscle with low reps and losing fat through lower calories. You get big by stressing your muscles with low reps and feeding them with high calories. In both cases, you want plenty of protein.