My method goes as follows:

First thing I do is capture all available information for a character. This includes all normal attacks, canned combos, and specials, and I document the following information:

Hits
Damage
Hit Type (High, Mid, Low)
Whether it's an overhead
Whether it's a pop-up that can be followed up

The next step involves documenting which hit in canned combos can be 2-In-1 cancelled into a special move. This varies per character and combo. Most allow you to cancel before the last hit, however, some allow you to cancel after the last hit. It should be noted, that a cancel after the last hit of a canned combo will never allow you to connect it on a grounded oppenent. An example of this is with Scorpion:

1,1,1 is a canned combo

In practice mode set the computer to block "Auto"

Now perform 1,1,1 -- it's 3 hits and counts as a combo

Now do 1,1, Spear -- it's 3 hits and counts as a combo

Now do 1,1,1,Spear -- it's 3 hits and blocks the spear. However, take note on how quickly the spear launches after the final hit. There is little to no recovery and you can immediately throw a spear.

Back to the combo building. Once you know what hits allows your character to cancel into a special, then I document how much damage is done on that hit. (this will be used for the juggle section of a combo).

Combos vary from character to character, but now with the information above, here is the general idea:

For max damage, start with a JP.

JP,

Now look through your list of combos and find the most damaging combo that either ends in a pop-up, or if you have a character that has a special move as a pop-up, use the highest damage combo minus the last hit, and cancel into the special that pops-up.

JP, Canned Combo Pop-Up or cancel into Pop-Up

Now experiment with how an airborne opponent reacts to certain canned combos--start with big damage ones, and take not of your characters recovery time (how quickly you can take another action). This will take some experimenting, but you should try partial canned combos, single hits repeated, etc. to determine the most hits/damage you can do before you can no longer juggle your opponent.

JP, Canned Combo Pop-Up or cancel into Pop-Up, Juggle Hits

Once you determined which, and how many hits you can perform on an airborne opponent, find a way to finish the combo. Because the game's engine is constantly making your opponent fall faster, and further away from you, the combo finish is usually something with decent range. Also, if you determine that you can do two sets of a jabs in the air before they fall, try doing just one set and see if you can do a more damaging full canned combo to finish (preferably cancelling into special for maximum damage).

JP, Canned Combo Pop-Up or cancel into Pop-Up, Juggle Hits, Combo Finish

Things to note: Dashing is a huge part of MK. Most large combos will require you to dash in between hits to stay close and deliver maximum damage. When experimenting, make sure that you are dashing to stay close through out the juggle phase of the combo. Also, if you have a canned combo that ends in a pop-up figure out how many times you can do it before the game grounds your opponent, also, find out if you can do a straight jump punch to re-pop them right after your original pop-up. This can add a couple percent to longer combos.

Characters are so different when building combos, so it's a little difficult to provide a universal template, but I think this will work for building decent combos with most characters.

If you have any questions about specific characters and their combos, please let me know and I can provide more specific information about cancelling, recovery, mix-ups, etc.

Hope that helps!

Awesome dude. Thank you very much, I just always wandered how one set out to create those.