Managing pics with software? Good idea!
I don't currently "manage" my pics with software per se, I currently use the operating sytem to do that. But I am open to the one perfect solution

I would like to hear about other systems.
This is what I do currently for organization/workflow for my pics. Workflow includes editing and uploading to photobucket.
In my mind I really don't seperate organization from workflow, unless I spend a lot of time on one picture.
After I have 20-250 photos (max that will fit on my 4GB card in RAW mode) I dump them into a
folder on my PC. Saving the original data is the most important step other than letting others and yourself actually look at the photos!
I put all photos on the card, or other containing media, in folders named after today's date, even if many photos are from previous days. The folder is named like this
yyyymmdd.
So a folder of pics dumped to my PC today would look like this: 20090912. The reason for this naming convention is that it always sorts alphabetically as well as by date! (learned this working with data and databases!) Also they are easy to find if a dump them to my laptop when away from my house.
I always dump them off my SD card (or dump them via a USB cable id I don't have my card reader for some reason) and then I try to remember to format my card before I start shooting again. Two reasons :
create space on the card and to prevent any
corruption on the SD card from continuing to the next set of photos.
====RAW mode Nikon=====
Once they are on my PC I look through them (obviously) with Nikon ViewNX to ogle ones that I really want to see. Any pic that does not have a problem (out of focus, overexposed, very inder exposed, etc.) I convert to JPG from RAW (.NEF in the Nikon world) into the same folder.
If I see something that I want to manipulate in RAW mode I will use ViewNX (free) or NX2 ($130) and do some digital darkroom work. I don't do any 'arts' stuff to my pics these days, maybe in the future. I just want them to be as to close to what I saw as possible.
====== in JPG mode ====
Once the JPGs are in their folder, I
rifle through them with ACDSee (really old version) or Paintshop Pro (really old version) to see what I like the most and may want to put on Photobucket or flikr or even email to someone! Also this is where I see if something went terribly wrong (thankfully it usually doesn't) if I did not see it in the previous step. ACDSee is nice because you can 'flip through a stack' of photos very fast by using page down, or you click wheel on the mouse. Once I see something I want to work with, I will open it up in Paintshop Pro. Another option is to browse a folder in paintshop pro, which lays out thmbnails of your pics in a grid like may photo programs do. I only do this originally if I have less than say 20 pics to look at because more than that may be too cumbersome. This is a basic editing program that I have gotten used to. I will do layering etc. but I am not interested in that for the most part unlees I am doing some kind of art (as opposed to the art of photography, with the camera). Paintshop Pro allows me to crop then resize bicubically if I want to. That's about all I do.
At this point I have RAW, and possibly multiple versions of JPGs in 1 folder. I see no reason to create subfolders in a dump folder.
PaintShop folder does not pick up the RAW files so that is convenient - I only see the files it can manipulate. ACDSee shows only the thumbnail file that is a part oif the RAW container file of the NIKON world.
But if I keep the pic files all in the same folder, they have to be
named appropriately to organize them and work with them. I have learned to always keep my RAW files named as the original files, or my JPGs if I shoot in JPEG mode. Then I never change the original name, I just tack on codes to the end of the name to create a new name. For example DSC_0186.JPG becomes 'DSC_0186
cropped.JPG' or more likely, 'DSC_0186
c.JPG'. If I then rotate it would become 'DSC_0186c
r.JPG'. If I had changed exposure previously to cropping and resizing or rotating it might be 'DSC_0186
daycr.JPG'. All versions of a pic are in the folder and I can find them by sorting within the folder if need be.
From this point I usually upload my favorites to the web. And get ready for my next shots by removing (safely) the card reader and putting the card back in the camera and formatting it.
This is also the time to back up that folder to another hard drive somewhere, preferably not on this PC. If not at this time, than at least weekly. My favorites are often already on the web somewhere, but not the RAW data! Once that is gone you cant get it back. You can always go through the folders and delete unwanted data later, but I like some time to pass before I make those decisions.
This leads me to think about hard drives. Get plenty! Hopefully you can afford more than 1 PC, with room for additional harddrives in each.
Alternativey you can get network storage which can be as expensive. Or at least an external drive that allows for quick-dock drives. Or all of the above.
With 1 TB drives under $100, there is almost no excuse. Also you can get a refurbished Dell PC with full warranty for under $400 with all the components. You don't even need a second monitor!
Also I often backup a valuable set of photos to a DVD disc. This is an alternative to a second hard drive but with time constraints I use a hard drive first. DVDs are a good third backup, as you can put them in a safty deposit box - but you will probably want check them every year! Same with harddrives!
Redundancy and separation are the most important things after the backup itself.
I want a better basic editing program (don't we all) but for now ACDSee and Paintshop Pro are what I have. Substitute anything here that works.
A reason for organizing this way is that I dont want to be tied to some company (Adobe, Apple, Microsoft...) that requires me to buy an upgrade just to keep my pics organized. My photographs will hopefull last for millenia

so I want to be able to handle them conveniently.
Also note that Adobe does not have the Nikon RAW 'algorithms' so I can't use the very popular Adobe programs to do some of this workflow

The good news is that Nikon's NX2 appears to be a VERY good program for working with thier RAW files.