I cant share the best practices, but I can share my practices. I am a photophyle, and very picky about how my photos are organized. I use iPhoto. I import everything into iPhoto and then delete the old file. (though for this first time, I would recommend moving those files to a storage device like an external hardrive or flashdrive instead of deleting them - just in case. Though i never needed to go back to those.)
Pros:
-It breaks down and shows all the metadata which I love! (i.e. it shows where the picture was taken, when, you can add faces to it - which ive done to all 13000 of my pictures).
-Easily syncs everything to your iPhone through iTunes
-Great organization, "folders" are spit up as "events" and you can easily browse through the pictures by passing your mouse over it without opening the event folder itself.
-Its just got cool features like slideshows and the ability to order custom picture books to be made within the program.
-All my photos are in one place "iPhoto library" file, so its easy to back up all my photos at once. So if you get a new mac, all you need to do is move over the iPhoto library file and you'll have your entire iPhoto library just as you left it.
Cons:
-With that last pro comment, the iPhoto file itself can become quite huge, and the backup will take a long while! (for about 13000-15000 pictures, mine is 40GB large)
-If you want to attach/upload a picture to a 3rd party site, you will have to drag and drop that picture onto your desktop first (makes a copy) and then you can use that one to attach to websites and stuff, then delete that picture from your desktop once youre done using it.