Don't know if you are still monitoring this...but here goes.
I remember the Ray Wininger(sp?) articles quite well. The Rules of Dungeoncraft completely revolutionized the way I run and prepare my games.
I am very fortunate in that my homebrew has been running continuously now since 1987. I say I am fortunate, because I continue to luck into some really great players (although there have been a few turds over the years) that really provide me with the right kind of support.
By some comparisons, I suspect that what I do is over prepare. Whenever I go to start a new campaign in my setting, I request that each potential player submit three to four character concepts and then I choose from their submitted concepts what character they will play. This helps to ensure long term party cohesiveness and it also helps me in 'bringing the party together' at the beginning of the campaign. This has proved very successful. I currently run two campaigns, one that is just entering its fourth year of play, and one that is only a few months old.
Another thing that I provide is a Player's Guide to the setting. This is a document that contains all of setting information that I have been able to put to paper, as well as home rules and whatnot. Another thing I do is collect feats, prestige classes, and other odd things from various hard-to-find d20 products and reproduce them in this document. This provides the players with single go to source for as much information as possible. This document also acts as a glossography and gazeteer to the world. Currently, my Player's Guide clocks in at 220+ pages, 9 pt Times New Roman with no graphics. My players seem to respond to it very well, and I find it is a great place to store all of my various home rules and rulings.
This document is something that I have grown, at my own pace, over the course of the last five years. So these things take time.
As far as NPC development, I keep track of important NPCs only to the degree that I absolutely NEED to. I never force myself to create more than I must, but due to the sheer time invovled I have volumes of information at my disposal, so again, this is the kind of thing that just ends up creating itself.
On the same lines as NPC development, I track relative power bases such as noble houses, guild unions, religious organizations, et al. I track what alliances have been made, and in the case of nobility, blood ties and relations.
The main thing I do for each campaign that I run, and there have been many with which I have been able to fine tune this process, is I keep a campaign story bible. Basically, I look at each gaming session as an 'episode' and each year as a season. I track the major stories I want to accomplish and based upon each character levelling about every three episodes or so, I can plan very far ahead. It also helps to have a regular schedule that everyone can commit to. It probably goes without saying that I am a bit of a gaming snob, and typically do not let players in who are not at least soemwhat committed.
This is probably my all-time favorite subject to discuss, but since this is a public forum I will limit myself. If you are interested, and want more feed back, just say the word.