Scenerio 1: The Weightlifter
I hear it all the time, "Oh man, my program rocks! I'm getting so big and strong! My bench is up like 20lbs in two weeks". Two months later I'll check back and it is always the same "Yeah, things are going well I'm getting bigger for sure." but when I ask how much they're numbers are increasing it is usually 20-30# above what it used to be, but it hasn't gone up any in the last 2-3 weeks. Usually in about 2-3 months they have plateaued doing there 3 sets of 10 or 15 and the 21's for the guns routines. At best they get a little bit bigger and a tiny bit stronger (on their 1rm). They can bench 135 for 15 but only 185 for 1.
They start doing high intensity workouts that only use light weights - P90x, Jazzercise, bootcamps. Now depending on the degree of couch potatoeness the atheletes will usually dramatic results for the first 2-3 month, good results of the next 3 months , ok results for the next 3 months and then minimal increases after that. eg. 1 Mile time goes from 11min to 8:30min to 7:15 to 6:45 to 6:40 to 6:38.
Now getting off you butt is good and doing something/anything is better than nothing. Now that being sad there is a reason that your current/old programs suck. It all starts off well because you are putting a stress on your body that it is not accustomed to and as a result your body needs to adapt to that change resulting in your increased speed/strength. But if this stress is the same - 3x10's or just body/light weight metcons, your body will adapt to it and you will stop experiencing gains. Now during this early period you will also benefit from increasing your muscle memory - the more you do a movement, the more efficient you learn to do it. Most of the time gains in metcons at 6-9 months in are due to this effect. Your stamina increases dramatically the first few months but during this time you are very exhausted during the workout and your form is crappy, making you inefficient. 6 months later your stamina is better and you are able to keep your form tighter and you start to become efficient in the movements. Doing a burpee 0.2 sec faster each rep over 50 reps is a 10 secs decrease in your overall time. Is your "cardio" better - no! Are you more efficient - yes! Are you therefore fitter - sure! Now efficiency is a topic for a different day but an important concept nonetheless.
Back to Adaptation - A good program is one that requires the body to adapt to new stressers and allows the body enough time and the ability to recover from the stress resulting in the ability to do more. Basically you need to do enough so that the body has to change/adapt but not so much that adaptation is impossible or too little that no adaptation is neccessary. The tricky part is that the amount of stress required for the change to occur and the amount of rest required before you have improved will change constantly during your training career.
For weight lifters - Use "starting strength", then move on to the "Texas method" then to a more advanced protocol. As you plateau you need to change the program accordingly nothing lasts for ever and what works for an advanced athlete will not work for a beginner and vice versa.
For P90Xers - Keep the exercises in your workouts varied and start introducing heavier weights. Switch to scaled Crossfit.com style workouts then try the real thing. For those long time body weight/light weight Crossfiters start getting heavier or increasing the difficulty of the body weight exercises try handstand pushups instead of regular. Do Fran at 115#, you can lower the reps at first to keep the volume similar to what you are used to. Your body will adapt and you will be stronger and faster. Get comfortable with being uncomfortable or risk being content with being scaled.
*Side Note: Doing 1000+ air squats in row is probably the dumbest thing you can do in your training as the stress is so high that there is no way you will see any gains after recovery in fact you will most likely see a lose in your abilities. Excessive/insane feats of strength will result in instant overtraining!