In order to give some context, I want to open by talking about goals. Most people do cardio for some combination of fun, performance, and fat loss. There is no "best" approach to cardio for fun, but the other two benefit from some kind of actual program design. Performance here has two sides (low-intensity and high-intensity, or aerobic and anaerobic), while fat loss only really varies with how much fat you've got left. If you've got a lot left, any cardio will probably work; when you're down to the last bits (what Lyle McDonald calls stubborn fat), things get harder. I'm going to focus on people at the leaner end...but first, let's talk about the performance side.
Cardio done for performance falls under what programming enthusiasts call GPP (general physical preparation) rather than SPP/SSP (special physical / sport-specific preparation). The idea here is that practicing exactly the way you play gets you good at the nitty-gritty bits (technique, etc.), but doing more general stuff (e.g. lifting weights, doing cardio) will get you good at all the stuff that's holding you back from practicing as well as you can. This is really important, because the stuff your body does to adapt for long-term aerobic work specifically isn't necessary as GPP for anything: it's specific to distance sports (SPP criterion #1) and can only be built up by practicing the way they play (SPP criterion #2). The cardio side of GPP for all sports centers around VO2 max (to stay as aerobic as possible for as long as possible) and lactate threshold (to stop the anaerobic portion from damaging performance). Both of those go up faster when you're working on anaerobic conditioning.
The other thing to consider here is what my (periodic) friend Jared Miller calls "bad day strength." It's a pretty strongly recurring theme with some of the better strength coaches out there: how good you are at your worst is just as important as how good you are at your best. If your football players are just good as the other guy's at the start, but drop to 50% by the second half while his are up at 75, there's a good chance he'll win pretty much by default. Same thing with boxing (except even moreso, at least in theory: see basically every boxing movie ever).
So, for performance we're basically after good performance in high-intensity activity that sticks around even once you're exhausted. Practically, that translates into intervals (generally regarded as the best way to build anaerobic capacity) done once you're already tired. It's the driving principle behind Liam Bauer's approach, and it works really well.
Unfortunately, that's not totally ideal for fat loss. The old idea with interval training was that it totally beat out steady-state cardio for fat loss by burning more calories after you finished than steady-state would during the workout. It turns out that that effect's only worth something like 50-100kcal per session, which while pretty nice (equivalent to an extra 5-10 minutes of steady-state) isn't that attractive given that intervals involve a lot of lactic acid release, and lactic acid impedes fat loss. There are still a couple of upsides that make it "better" than conventional cardio, though, and to cover that I'll open with some (primitive) physiology.
We've got two hormones (and an acid) that we care about here: adrenaline/epinephrine, noradrenaline/norepinephrine, and lactic acid. Noradrenaline is that stuff that gets you jittery when you take caffeine, and gets released mostly into small blood vessels via nerve endings; adrenaline's the one that sets you up for fight or flight when someone pulls a knife at the club, and goes through general circulation. Both tell fat cells to dump fatty aids into the bloodstream so they can be used as fuel. Lactic acid "traps" fat in fat cells regardless of hormone signalling.
Low intensity cardio only prompts release of noradrenaline but doesn't put up much lactate, and does allow your body to utilize fatty acids for fuel. It works best when you're getting close to lactate threshold (basically the dividing line between low and high intensity), and does "ok" for handling most areas of fat loss. Unfortunately, your body also adapts to it quickly by both reducing the calories you burn while doing it (less fat burned during exercise) and your overall metabolic rate (less fat burned for the rest of the day). Since your metabolism's already dropping if you're eating less, that's a problem. High intensity work (generally done as intervals) throws out huge amounts of lactic acid and both hormones, giving you very little fat burn during exercise but a big spike in fatty acid release once the lactate drains off. The cool thing is that your body doesn't drop metabolic rate to adapt to it (and actually elevates it slightly); it probably doesn't drop the calories burned during exercise either, but that's less meaningful since you aren't burning fat during the exercise (though more of the food you eat later will wind up replacing the stuff you did burn, which might explain some of the metabolic boost).
So, for early stage fat loss, Bauer's thing actually looks pretty much perfect: we do some low-intensity work to warm up, some work up near lactate threshold to tire ourselves out, cool down for a few minutes, then jump into intervals, then cool down and go home. The intervals progress incrementally and drive performance up.
So, Bauer's Interval Training: Great for performance and fat loss.
But after a while, we run into a problem. Bauer's program lasts 12 weeks, and after that you basically just keep going but change the activity every few weeks to keep your body guessing. You can keep progressing on the 20/10 intervals (which are absolutely brutal), but as you get leaner and leaner, you eventually come down to the "stubborn" fat areas that respond poorly to isolated low-intensity work.
The stubborn areas don't act the way the others do. First off, they close off when noradrenaline binds to them instead of opening up (adrenaline overrides this), and second, they have very little blood flow, so when they do release fatty acids they normally take them back up pretty quickly, resulting in minimal net fat loss. Low-intensity cardio can shrink them down (especially near lactate threshold), but it's pretty bad at it thanks to the noradrenaline thing. Intervals alone (or at the end) also don't do that good of a job, since the fatty acids that do get released just get reabsorbed instead of burned.
Lyle McDonald's solution here (nicknamed the Stubborn Fat Protocol) handles this with a modified plan. Now, you start with intervals to jack up adrenaline and set up that delayed fat release, downtime so the lactic acid can drain off, then steady-state work near lactate threshold to get blood pumping (wash the fatty acids away from the fat cells) and keep adrenaline high (maximize fat burning and try to keep the stubborn fat cells releasing their contents). It's basically Bauer's thing done backwards, and supposedly works quite well. It's also totally pointless if you're not already very lean. Stubborn fat stays off-limits until everything else is gone (hence stubborn versus just "slow"), so there's no benefit in trying to hit it early. Bauer's thing has you burning the "easy" fat cells twice (once with the low-intensity, once again with the aftermath of the intervals); the SFP's based on the idea that that just doesn't work for stubborn fat.
There are also some tricks you can do for the stubborn fat. Restricting carbs to less than 20% of total intake can help improve the hormonal situation (lower insulin helps fatty acid release, and low-carb diets also boost adrenaline and noradrenaline release), even if you stay out of ketosis. Caffeine and L-Tyrosine intake help with adrenaline and noradrenaline levels as well. Most importantly, Yohimbine HCl (dose at 0.2mg/kg - e.g. 15mg for me as a 160-170lb guy) blocks the receptor on fat cells that makes noradrenaline switch off fat release (thereby effectively boosting noradrenaline levels). You want to time the Yohimbine carefully, though - if it hits your bloodstream during the intervals, you will feel like you're going to die. Take it 20-30 minutes ahead and it should hit right as you start the steady-state.
McDonald also has a more intense program ("SFP 2.0") that aims to the metabolic boost going. He has a hunch that the original SFP deprives you of the long-term metabolic boost of the intervals (since you're doing steady-state right afterwards); not huge, but useful if you're after the very last spec of your external fat. The solution there's pretty simple - just split the intervals up. Shorter intervals with longer rest do a good job at the start, since they let you push adrenaline up without keeping really high levels of lactate (better fatty acid release after the break). They also make the later stuff a little less hellish. The "longer" intervals seen towards the end of Bauer's progression work really well for the end period, since they prompt a bigger metabolic boost after you finish. One modification here is that long/short on intervals refers more to the ratio between high- and low- intensity periods; 30/30 is "shorter" than 20/10 just because you have more time to recover.
Oh, and remember "Bad Day Strength?" It's hard to beat doing intervals twice in half an hour.
The extension on this is that after a while, you're going to have gotten rid of that last bit of bodyfat and started dieting back up (see Layne Norton's stuff on reverse dieting). Since you're bumping calories back up and focusing on metabolic rate rather than fat loss, you've now got a great excuse to hammer the intervals a bit differently. My guess is you'd be best off moving along with 2 weeks each at 5x20/40, 5x30/30, 5x45/30, 5x60/40, 5x90/60 so you're really hammering the different energy systems.
The final fun note here is that Bauer's approach actually melds into SFP 2.0 really nicely: get to the end of Bauer's 12 weeks, sit tight for a bit to get used to the ridiculously vicious intervals you're doing, then just switch to SFP 2.0 with 5x15/45 for the first run and 10x20/10 (same old Bauer) for the second.
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