I use Apple's Aperture. Not available for PCs, unfortunately, but there it is. I'm sure 99% and then some of what I can do in Aperture can be duplicated in any other system. Adobe's Lightroom is analogous, and available for Mac or PC.
The very first thing I do is cull out all (well, most...) of the really poor images before I pull the card from the camera. This can be problematic, if you have an older camera with a small LCD on the rear. I shoot primarily wildlife, mostly birds, so some of the things that go before the card ever leaves the camera are:
out of focus
motion blur (unless desired in the final image. Birds can be VERY fast!)
bird facing away from the camera
shots of my trouser leg when I set the camera down on my knee, on the shutter release with "full auto" set.
And many more...
Some of these I may import anyway, like if I only got a few fleeting shots of something in the woods, so I can use them to ID the bird later. It's variable, depending on where I was, etc. I use image zoom a lot. Beleive me when I say almost ALL images look in focus when they're 18 MP images shown on a sub-1MP LCD! I'll also do several passes in camera. I can't really get a feel for the good and bad images in one run through. I'll do two, sometimes three passes (the more images there are, the more passes I'll do, usually), and usually in both directions (oldest to newest and v-v) before going to the computer. Especially with something new, or with particularly good conditions, I tend to take a lot of shots, but only 50% (and often less!) are really good. Culling out the bad images in the camera is one of the top 5 things I like about digital.
The next thing I do is to try to import as close to the event as possible. I don't wait for a full card, though one event may span multiple cards!
Third, In Aperture, I use "Projects" to organize the photos (there are other methods, such as folders or libraries, but this is the one I use). Each Project is named usually according to the event (in the case of a Saab tour & picnic, or any one-day event), or the place (in the case of a Wildlife Refuge I frequent).
Fourth, when I import, I select the project that the images go into, and I can also change the name. I can set the name to be whatever I like, and add things like the date, a counter, etc. So if the file name is IMG_0123.CR2, when Aperture finishes the import, it might be called "Great_Swamp_NWR_2012_06_25_012.CR2". This gives each imported file a distinct name, and, even better, if you somehow saw the file by its lonesome, you'd have some idea of what is in it!
Aside: You really need to use this feature in whatever program you use. ALL cameras will reset their counters after 10,000 shots usually, so it'll go from IMG_9999.CR2 to IMG_0001.CR2), and you can easily have multiple images with the same name.
Fifth, in the same Import settings pane, I can (and do!) tell Aperture to copy the RAW files to a separate location. So, when the import is complete, I have three copies: one on the CF card, one in the Aperture Library, and one on a separate drive. I can then format the CF card(s) for a new shoot.
Lastly, Aperture gives me the option of maintaining a Vault of the images. The difference here is that a Vault contains all of my edits to the images, where the backup made at import contain no changes. I can update the vault as I make changes. My vaults are contained on a third physical drive.
One note about Aperture, Lightroom, and some others, is they are non-destructive programs. You will always have the original to fall back on in case you do something silly like turn all your family pics into cyanotypes... It stores your original, and all your edits are stored in a separate sidecar file. This is unlike some other applications, which are destructive editors, and changes are made to your originals, and you may not be able to go back to the original.
There is also a concept called "Managed" libraries versus "Referenced" libraries. A Library is simply the file (database) where your images are stored. "Managed" refers to a library where your originals are actually stored inside the library file. This can be very handy, and you only ever see the one filename for the whole library, whether there is one pic, or 100 thousand in it. "Referenced" refers to a library where the originals are stored in one location in the normal file system. The library database keeps track of where the original is, and also keeps your edits in the library. Some folks like this because it's easy to visually see all your stuff. The one drawback is that you can accidentally move or delete an original, and then the library doesn't know what to do about it. I don't particularly think one way is better than the other, and some folks use both, or one exclusively. This is one of those Coke vs Pepsi debates, where there is no real answer, just your own preference (I prefer managed libraries. And Coke... ;-)
Of course, I still commit the ultimate sin. Even though I have my images on at least three different devices at a time, they're ALL on my desk at home! Not really a backup strategy, but it somewhat protects against drive failures...
Poke around the web. Plenty of places to look. Check out photo<dot>net. Lots of photogs there with all manner of equipment, and post-capture workflows!
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