RE: iPhoto
I have found it useful to keep a backup stored elsewhere (external HD, Time Machine, CD, DVD, etc.) and to import images directly to iPhoto. Once they are in the application, you should ONLY modify them using the application itself; you can remove modifications and get back to the original images within iPhoto. If you need to edit any of your photos outside of iPhoto (I do this regularly), the best way I've found is to EXPORT the image with your desired resolution and file format, then open the image from Photoshop, Picasa, or other program. I've found that each program has it's strengths and weaknesses, so certain tasks may be best accomplished on one or another program.
If you modify images directly in the iPhoto folder (deleting, renaming, copying, moving, etc.) you will screw up the iPhoto library. It will become 'corrupted' and you'll start to see 'blank' icons show up instead of your photos. You can 'rebuild' your library, but it isn't a perfect process.
Also, iPhoto makes it easy to create backup disks from within the application. That way you can safely import all your photos into the program, then create disks with the originals to be filed for safe keeping.
If you have many photos stored (as I do), you will probably want to get the iPhoto Library Manager. This allows you to have separate libraries rather than 15,000 Events.
http://www.fatcatsoftware.com/iplm/
It is available free as well as with advanced features for $20. Well worth it if you deal with lots of photos.