First of all, first post 

Ok. Now to the matter at hand.
I've been playing around with how I want to organize my workout lately, and I've got a few questions that I wanted to get some opinions on. Articles are nice, but personal opinion or experience is really what I'm looking for for now.

<First some back-story>

After having some very minor issues with my knees, I started to look at the way I was training, because I'd done significant rest to the point where they no longer hurt, I was watching my actual parkour training to make sure I wasn't putting undue stress on my joints, but still they hurt after some time. So I started to examine my workout regimen. During that time I would do (just to focus on one exercise)  three sets of 75 squats per day, probably 4 days a week. As I thought about it, I was like, "Hm. I know the human body is made to do squats, but probably not that many all compressed into just a small amount of time."

<Now some info on what I've decided to do.>

I settled on 25 as my maximum number of reps per set for any exercise that uses a major joint in excess (squats, push-ups, pull-ups, etc) for my first tier. I figure I'll bump that to 50 after a good amount of time to strengthen all my joints and muscles.

Why? What are your goals? If they're anything like strength and power then 25 is not effective at all.

Goals come first; then structured programming.. not the other way around. I detailed this in the "How to construct..." article.

But now the question remains -- how long should there be between sets to still be effective?

This depends on goals

The way I think of it is what would be natural; what would we do if we were thrown into a completely natural lifestyle? The conclusion that I came to is that exercise is probably not crammed into 1-2 hours in a single day. I imagine that if someone were to drop you out in the woods and told you to survive, your daily activity would probably not be a single moment of extensive work in a short amount of time. It would probably be a smaller amount of work, but repeated over and over again throughout the day.

What if you're a hunter and everyone else at your camp is doing chores; you go out to chase and kill the beast and haul it back. Certainly this is just an hour or two.

This argument makes no sense at all.

With that in mind, I came up with this: I designed four groups for exercise on a day to day basis (outside of extra training I do during parkour sessions): upper body, lower body, core, and movement. Each one contains between 5 and 7 exercises that I chose because they emulate movements that I would make during parkour or during the day. For example, I included palms-out pull-ups, but not palm-in pull-ups because I cannot think of a time when I have EVER lifted myself to a certain level with my palms facing towards me. I roll a die twice to get two numbers between 1 and 4 that choose which of the four groups I'll be doing that day. Then I have a total of 5 sets; three of the first group, and two of the second that I MUST do during that day (extra sets if I'm bored with nothing to do and would otherwise just sit at the computer are welcomed). Then those 5 sets are spaced out into 3 parts of the day: soon after I wake up I would do 1 set of both groups. In the middle of the day I would do 1 set from the first group, and at the end of the day, 1 set of both groups.

<And now the question.>

I've just started this recently, so I can't attribute anything to results, but I can say that after each day that I do feel what I've done throughout the day. Has anyone else ever played around with exercise over an extended period of time? Is 3 sets of 20 push-ups done in 3 minutes really any better than 3 sets of 20 push-ups done over the course of the day? Is larger amounts of exercise done in a shorter amount of time better for you than keeping yourself active over the day in smaller increments?

Yes, different rest times and spreading out work leads to different results. Hence, why we program with GOALS in mind.