Now this link will provide a wiki article about all the different kinds, but I'm going to introduce you to my three favorites. There's Ahnentafel which starts from the end and works it's way backwards to the beginning. This one's nice since you'll see how each surname combines into the next generation. Most published works deal with a single surname from the progenitor down to the latest generation. A standard system I've seen in books about my family has been the Register Style first made for NEGHS. Emphasis is still given to those who've been productive- so those who've died young or without descendants may not be listed/numbered. Then there's the d'Aboville system that gives each person a unique number based on generation and birth order. I have one list for each surname I'm tracking and I add as I go.
Ahnentafel is very popular. This one begins with the descendant, say my Grandfather Householder, and goes up through the ancestors. A person is assigned a number, 1 for the root. Then the father is double that number, 2. The mother is double plus 1, 3. So the men will be even's; the women odds.
1. John/Andrew Gibson
1.1. Joel Gibson
1.1.1. Burgess Gibson
1.1.2. Robert Gibson
1.1.3. Greenberry Gibson
1.1.4. Margaret Gibson
1.1.5. Bailey Gibson
188.8.131.52. Joel Gibson
184.108.40.206.1. Mary Gibson
220.127.116.11.2. George Gibson
18.104.22.168.3. James H Gibson
22.214.171.124.3.1. Fannie Frena Gibson
126.96.36.199.3.2. Zackariah Gibson
188.8.131.52.3.3 Marcus Tilden Gibson
In this example from my Gibson line, my great grandfather Marcus is the third son of James. James is the third son of the first son of the fifth son. I add the wives/husbands in with a +, but they each have their own ancestry list if I've traced them farther back. I'll carry the daughters down to their children, but any farther and it gets it's own list via the patronym. If I ever find out more about John/Andrew Gibson, it will be easy to add his parents to the top of the list and add a number to the front of everyone's lines. If I discover a new child for someone, I can add them and make a few adjustments as I go. In the end, I'll probably publish my work using the Register System, but I keep myself on track with the d'Aboville system.
Whatever you choose, stick with it. Consistency is key to organisation. Work what works best for you. Numbering systems can really help you keep the larger picture in mind. And starting your organisation from the off-set of your family research can keep you from having to go back and do it later..... ya know, when it's grown so big you'd become overwhelmed?