I'll make a couple of very simple suggestions which will save no end of issues.
1. Rename to a unique name at the time of import, and then don't rename it again. A dated filename such as YYYYMMDD-HHMMSS (year, month, day, hour, minute, second) based on the Capture Time is ideal for that. The simple reason is it makes it easy to go back to backups if you need to, and it means you never accidentally overwrite photos.
2. For really easy backup, use a dated folder structure i.e. YYYY/YYYY-MM/YYYY-MM-DD so you can easily see which folders are new and need backing up offsite.
3. Back up to hard drives rather than optical media (apart from possibly a first import backup to optical) as you'll save yourself hours. Automate it using file sync or backup software.
4. Don't duplicate the same photo in different folders (i.e. a photo of Jane and Karen needs to be in a single folder, not in a Jane folder and also in a Karen folder).
5. Use Metadata like keywords to find the contents of the photos - i.e. store them in dated folders (and by all means add a descriptive phrase like Kate's Wedding to the end of the folder name) and add keywords to show that the photo includes Jane, Karen, Kate, Fred, it's at a wedding, and the dresses were blue. I'm not usually a fan of keywords, but this is the one place I highly recommend them.
As far as software goes, I'm clearly a Lightroom fan. It's not always the most intuitive program, but it's well worth the effort to learn it. If you want something a little lighter, the Photoshop Elements Organizer isn't bad. Picasa's ok but it tends to have a habit of hiding your photos from you, and has been known to write non-standard metadata, which I tend to shy away from.