When you do your training is not nearly as important as just doing it consistently on a pre-planned schedule, with meticulous attention to progressive overload. Timing is a secondary and in my opinion, a highly overrated factor. Don't lose sleep over this or get caught up in the arguments either way.
The very first thing everyone needs is to establish a pre-planned training and nutrition schedule that is so regular that training and eating on a routine become habits as deeply entrenched as brushing your teeth, taking a shower, driving a car, or putting your pants on with the same leg first every day. Training and nutrition can eventually become so habitual that they turn into automatic behaviors requiring no conscious thought - and that is a great place to arrive at. For someone still struggling to overcome bad habits or stick to a regular schedule (i.e. you're still skipping workouts or eating junk), the workout timing issue is moot.
Once you've developed that kind of consistency and regularity in your training and nutrition habits, then it pays to start nitpicking and tuning the fine details - and yes, one of those details is workout timing and meal timing.
The ideal timing of training depends on (1) your goals (fat loss versus gaining mass) (2) practical considerations like job, family, and time available, and, (3) whether you are doing cardio only or cardio and weights the same day.
First, lets talk about fat loss. When fat loss is the goal, I believe that 30 minutes of cardio first thing in the morning on an empty stomach has many benefits.
What about if you're on a fat loss program and you're doing weights and cardio the same day? You have a few good options. One, do your cardio only early in the A.M. on an empty stomach, then eat meal one immediately afterwards. Hit your weights in a separate session later in the day - late morning, afternoon or evening. Two, since working out twice a day isn't practical for everyone, eat meal one, then do weights and cardio in the same session, with the weights first and cardio second, followed immediately by meal two. If you're doing both in the same session, DO NOT do cardio first followed by weights or your weight workout will suffer greatly.
On a mass gaining program, things are different. I DO NOT recommend morning cardio in a fasted state on mass programs. In fact, I recommend a minimum of cardio on a mass gaining program: 3-4 days per week for 20-30 minutes and that's it. Extreme "hard gainer" ectomorphs (skinny, small jointed body types) should do even less - more like 3 days per week for 15-20 minutes (if any). On the mass gaining program, split up your cardio and weights if possible, and space them out a good eight hours or so (lift in morning, cardio at night, for example). Eat plentifully after each workout session. If you must, simply hit your short cardio workout immediately after your weight training workout.
By the way, the twice a day schedule isn't practical for most people with 9 to 5 jobs, families, etc, etc, but if you can swing it, it has several potential benefits:
1) It allows you to get a meal immediately after your weights, which maximizes recovery and muscle growth (extremely important if muscle mass is one of your goals).
2) It gives you a double boost in metabolism instead of a single post exercise metabolic increase (like spinning a top twice within a certain time period to keep the rpm's going faster instead of spinning it only once and letting the rpm's slow down before spinning it again)
3) For fat loss programs, it allows you to get the benefits of fasted morning cardio
4) It gives you more energy for each individual session, instead of one long, energy-draining session. When you do weights and cardio together, whichever you do last tends to suffer because your energy levels start to decline (just try some high intensity interval training after your 20 rep squat routine!!!)
5) It maximizes hormonal response to exercise for maximal fat loss and muscle growth.
6) It minimizes the possibility of overtraining.
If two sessions a day doesn't fit into your schedule, then doing your cardio immediately after your weight training is also effective. The only drawback to doing weights and cardio in the same session is that the workouts can become very long and tiring; sometimes 75-90 minutes (for example, 45 minutes of weight training, followed by 30-45 minutes of cardio).
Some people are terrified about the possibility of losing muscle when doing long training sessions of weights and cardio together. Ironically, the worrying probably causes more muscle loss than anything! Worry and stress are highly catabolic. Instead of worrying, simply measure your body fat, chart your progress and keep a close eye on lean body mass. As long as you're not restricting calories too severely, you'll probably discover that you maintain your LBM just fine. If LBM drops, then think about changing your workout timing.
There's probably some truth to the assertion that each individual has a certain natural biorhythm which dictates their personal best time to train (morning people vs. night people). There may also be some truth to the theory that metabolic rates and hormone levels at certain times of the day or night make for better results if you train in harmony with these ebbs and tides. I am an early riser, but I am NOT a "morning person." I experimented one season with eating meal one, then lifting at 5:30 am and my workouts suffered terribly - really, it was awful - and I gave it a fair trial for three months straight without missing. I was not mentally or physically primed to train at that time.
The logical, theoretical, left-brained types can go ahead and pooh-pooh the "instinctive training" principle all they want, but I don't care what scientific study comes out saying that training at 6:00 A.M builds more mass, I KNOW early morning lifting isn't for me. When I'm training for contests, I prefer doing cardio at 5:30 or 6:00 am, then meal one, then meal two, then hitting the weights at around 10:00 am or 11:00 am. This works great for me because I work 12 or 1 pm to 11:00 pm. If you've discovered a certain time that "feels" good to you, go with the flow and don't fight it.
Let me re-emphasize again, I think the importance of this topic is blown way out of proportion. In fact, sometimes I'm sorry I wrote that morning cardio article because it stirred up tons of controversy. Judging by the number of times I've heard questions about morning cardio and workout timing, people are very concerned about doing it wrong. My advice: Just get your butt in the gym whenever it's convenient for you, get on a regular schedule and train hard, hard, hard. Then go home and eat, eat, eat your lean proteins and complex carbs from natural, whole foods. Getting lean and muscular takes effort, but the process is really not that complicated... honest!
Training is covered in detail in my 340 page ebookBurn the Fat, Feed the Muscle (BFFM)
Also, be sure to check out my new ebookFitness Over 40
If you do not like to read I have a brand new 6 hour audio series BurntheFatAudioSeminar.com