I find Deadlifts and Squats to be the most strenuous exercises. It makes sense, because these two are strength-builders - not calisthenics - and engage so many muscle groups at once. (In the Calisthenics category, I find Burpees the most strenuous.)
Squats are a fundamental, functional, whole-body exercise. As it is wrong to say that Deads can hurt your back, it is wrong to claim that squats can harm your knees. The contrary is true for both.
I focus on the squat today as I have begun to introduce weighted squats into my basic strength-building routine. I need them. Barbell on my shoulders works best for me, but to each his own. Kettlebell held on chest is good for a start.
8 Reasons to Do This Misunderstood Exercise
How to Do the Perfect Squat
It has taken me 11 months to get this olde corpse of mine into good enough condition to wean almost entirely off the machines and to be able to limit my strength-training with the good old basics: dumbell variations, pull-ups, bench press variations, squats, deads, and the like. (Can't do push-ups due to shoulder injury. In middle age, if one has led an active life there are always physical flaws you have to work around.)
As I have said before, my weekly 5-6 day routine includes a mix of cardio intervals, strength-building, and heavy calisthenics. It is a war against apoptosis, entropy, and Father Time. Thus it is bound to fail, eventually. Lucky for me, any issues I had with fat resolved in my first few months of training - now just the normal issues with strength and endurance that many sedentary middle-aged workers have.