It's intuition at a certain point, but if you're doing sets of 20 or more...then it's beyond time. I normally would suggest increasing difficulty if you can exceed 12 reps of any exercise that uses a rep system (as Isometrics must be treated differently.)
You should certainly check out http://www.eatmoveimprove.com/2010/03/the-fundamentals-of-bodyweight-strength-training/, because Steven and Chris have assembled some very useful information for bodyweight work. If you're really into it, Steven has written a book on the subject of bodyweight work.
There's always a great deal to learn, and after you've reached a certain level of training...you'll be able to spot good and bad plans on your own, be able to use intuition to determine what you need to be training, and just know when you're ready for new skills. When you're in the beginner and intermediate levels of training it's good to use the sense of people who have been there to help guide you to not make some of the same mistakes that they did.
So I'm reading that article by Steven and Chris. I feel as if I should tack on a little more to my routine, and reduce reps but increase intensity.
Here is what I have so far:
Upper Push:
4x3-8 harder difficulty push up variations (Any suggestions? I do about 40 pushups flatground, and somewhere around 20 with feet on a basketball)
Planche progressions (Starting with frogstand, I can do one with bent arms for about 40 seconds. I want to get it with straight arms, though)
Upper Pull:
4x3-12 pullups of higher intensity (I might need to buy resistance bands?
Inverted Rows work (I need to find somewhere to do them and I'm not quite sure what I can do with them now)
Flag stand work?
Legs:
6 or so 100m sprints (I usually leave this to the end because I have asthma and this kicks my a**

)
Box Jumps till exhuastion (Do I need resistance bands or weights to make it harder? I usually get about 30 till im tired, but i usually dont give up till 40-50)
And One Legged Squats (Building into pistols)
Core:
1x30 sec RKC plank
1x35 sec RKC plank
1x40 sec RKC plank
1x45 sec RKC plank
Skill work:
Working Handstands (5-10 minutes)
L sit works (Not quite sure what I can do with this yet.
Flexibility:
Splits work
+ other warmup exercises and stretching
Goals:
Be able to do the splits (Shorter term)
Be able to hold a planche (Longest term goal)
10 consecutive pistols with good form (Medium term)
Be able to hold a flagstand for 15 seconds (Medium term)
30 second free handstand (Short term)
10 good 1 arm pushups (medium term?)
10 good 1 arm pull ups (medium term?)
I just really need suggestions for increasing difficulty of my push and pull exercises. I'm guessing I should just buy resistance bands and weight I can put into a backpack or something? I'm also going to be looking into buying some training rings for my pull work.
Anyone have thoughts on my new routine?
Another good resource is a book called Convict Conditioning. You can find at at Dragon Door's website. It's slightly pricy, but definitely worth every cent. It's got progressions to get up to the big six bodyweight movements: the pistol, the one-arm pushup, the one-arm pullup, the stand-to-stand bridge (really cool to watch), the one-arm handstand pushup, and the hanging leg raise. Anyway, it's a great program. Since I'm such a big Pavel fan, I might as well also plug The Naked Warrior. It's another book about bodyweight strength on Dragon Door.
I'll look into it!