To give you some idea of my process, last generation I finally sat down and sorted the boxes according to types then sorted the pokemon within them according to number separated by type.
This kind of sucked.
The normal and water boxes were full to overflowing and required multiple boxes while ghost or flying were completely empty leading me to consider moving the typical pidgey-esque schlock into the flying box despite that not being the first type listed in their summary page.
http://bulbapedia.bulbagarden.net/wiki/List_of_Pok%C3%A9mon_by_evolution_familyIdeally I'd like to sort by evolution family and numbers not unlike the bulbapedia chart linked above! If I don't get better ideas from this thread I'll probably set about translating that page into a plain text file or maybe RTF so I can easily build a chart, add more to the document with new generations, and maybe quickly and easily mark which pokemon families I already have a member from and which ones I don't.