Yeah, I'm in this position. I've been using the machines at my gym (more for variety than any other reason) and when I started looking into strength training, I was swamped with competing methods, many of which instantly sent up red flags in my brain reading "SCAM".
It's difficult for someone from outside the fitness world (me) to judge whether a method is legitimate or if it's simply the fitness equivalent of a get rich quick scheme.
Lift heavy shit over your head. Put it down. Repeat.
To this end, barbell training is pretty much the gold standard in gaining strength. Machines are suboptimal in that they stress muscles in isolation from one-another, and remove the need for compound, coordinated muscle contractions that occur in literally every situation where you would want actual strength. Proper barbell training with compound lifts (squats, deadlifts, overhead press) trains whole groups of muscles at once, including the crucially-important stabilizers which are often neglected in machine-based training.
Starting Strength and Stronglifts are two extremely similar barbell training programs with a very large number of success stories. I've been doing the Stronglifts routine for three months, and am transitioning into Starting Strength as I make my way through the extremely thorough book (which goes into extremely helpful detail about performing the lifts with correct technique). In three months, my squat is now 195lb, deadlifts are 235lb, overhead press at 90lb, bench at 125lb, and barbell rows (which I'm phasing out in favor of power cleans) at 125lb. And I continue to add weight almost every single time I go out.
The numbers aren't super impressive by themselves, but for only three months from having starting at the weight of the empty bar (45lb), I'm seriously thrilled.
I recommend you read this archive of Bill Starr articles: http://billstarrr.blogspot.com/
He taught Rippetoe much of what he knows back in the day. I think Starr articles are way more readable and useful than most of Rippetoe's stuff to be honest.
In general, you should mix cardio work with lifting heavy things. The ratio will depend on your goals, as will the kinds of lifting you do. All things being equal, exercises that involve more muscle groups and larger ranges of motion will burn more calories than isolation lifting (which is what most machines are set up to do). If you have weak joints or other physical constraints, machines can be a good place to start, as they will provide you some degree of support and help with your form.
Part of the reason you hear about so many methods is that so many of them work. Most are greatly oversold, and in the long run you'll find out what works best for you and ignore the cookbook-style exercise plans, but anything that motivates you to create a fitness plan and stick to it in a disciplined fashion is a good place to start. In fitness, consistency creates more progress than efficiency, and premature optimization is still the root of all evils.
This is one of the main reasons I've stuck with the machines. I have a rotator cuff issue in my left arm that makes that arm very unstable. Lifting heavy things with that arm without any support makes me very nervous, even after doing PT exercises for 4 months.
The reason for this is because many machines have a set path and range of motion. Because not everyone's body is made the same, this can cause problems down the line since the movements are not natural. You are also recruiting less of the smaller muscles in your body that help with stability and balance, while only developing the larger/dominant muscles. I believe that to truly be strong you must train all your muscles to work effectively as one system.
Obviously limitations from injuries are extremely specific to the individual, so your issues may legitimately cause some barbell lifts (particularly bench presses) to be a bad idea. But I do also personally know of a lot of anecdotal evidence that points to freeweight exercise reducing the impact of people's injuries: e.g., knee pain from squats in a smith machine disappearing when performed in a power rack.
Be sure to read the FAQ there. The TL;DR version is to pick up one of the two programs mentioned above (5x5 or starting strength).
I've noticed men avoid these classes because tend to be a majority female attendance (at least at my gym). I do feel like the classes are also geared towards women, but that could just be me or my gym (they call is body-design). I'm not intimidated by that, but I feel like many guys are.
I do these with my girlfriend usually, which helped get into it initially, but I'm often the only guy. Doesn't matter, it's a killer workout. Even though I lift, I still do classes like this each week for general fitness.
What is safe to have at home? I want to avoid a resistance machine or similar, mostly because they look ghastly, and secondly seeing so many on CL leads to believe they are more hype than health.
You can do squats safely without a spotter by using a squat cage. Also, when you place a bench inside of the cage, you can use catch bars to safely bench press without a spotter (the safety bars will catch the bar at chest level when you can't lift it due to exhaustion)
Along with pull ups, bench press, squat, and deadlift are the best exercises for strength. An olympic bar will let you do both deadlift and squat with just a rack.
Just to add that 'safely' in this context means that if you fail at a rep, the cage will catch the bar. Obviously it can't do anything to point out bad form as a spotter, or even a mirror, could.
I use the squat cage at the gym I go to and I wish they had more mirrors. A pair of angled ones so I can see a side-on view would be really helpful.
A mirror only shows the front of you. If you stop looking into a mirror, you'll find that your ability to "feel" your form through proprioception becomes significantly stronger. And it will tell you things that you simply cannot view in a mirror. Try doing an entire session without using mirrors; if you find it difficult or impossible to maintain proper form, that should be an extremely compelling sign that the mirror has become a crutch, and not a very good one.
There's also the unfortunate fact that, by looking into a mirror, you're guaranteeing that your head is tilted farther back than it ought to be for exercises like squats. You never want to have your neck extended while carrying a significant load. It should be in a neutral position — for a squat position, this will equate to looking at the floor roughly five or six feet in front of you.
With just a weight set you can learn to power clean, do front squats with decent weight, zercher squats http://www.youtube.com/watch?v=tq1maZuQTgI jefferson squats/deadlifts. Can also do floor press or put some planks and books under yourself to get full range of motion.
What kind of weight set, power rack, bench to buy you can discuss in equipment forums like http://forum.bodybuilding.com/forumdisplay.php?f=26
Spinlock bars suck though, low weight capacity and annoying to use.
I'm about halfway through the book and I would highly recommend it.
It really simplifies things in the weight room, points you in the right direction, and says "now go do this."
It's pretty much gimmick free, and very straightforward. Highly recommend it.
I'm currently looking for a correctly equipped gym near my apartment in Paris, France. Looks like free weights are not fashionable at all here ...
It's popular so it's bound to have critics.
Beginners can often become overwhelmed by all the differing viewpoints and training methods presented to them when researching strength training but (besides avoiding injury by maintaining proper form and generally listening to your body to allow sufficient recovery time) the most important thing by far in anyone's fitness lifestyle is simply consistency in actually working out.