I had major problems with iphoto about 6 months or a year ago, I can't remember exactly when it was. I had imported around 2,000 photos at that time, and had them all nicely set up in albums.
One day, about half of them were gone! The albums were gone and the photos were also actually missing from my iphoto library.
I panicked of course as I had not done a recent backup (doh!). However with some help (can't remember if it was here at macrumors or on the Apple discussion boards), I found that my photos were in fact still on my hard-disk somewhere in the iphoto folders but were not being recognised by iphoto. I tried all sorts of things to recover the photos - can't remember exactly what, but I think it was renaming or recreating the library or something. Anyway, it didn't work.
I had to completely start again and reimport all my photos from the folders on my harddisk. I lost a lot of the ordering and albums but at least I had my actual photos. Someone from Apple told me that this had happened because I had messed with the contents of the iphoto library folder, but I deny this. I had never been anywhere near that folder until after the photos disappeared. I simply did not do anything and the photos just disappeared. I understand this has happened to a lot of other customers but that Apple has not been able to properly identify the problem or produce a fix.
What I now do is copy my photos directly from my camera to a folder on my external hard-disk. I give the folder a name that makes sense to me - e.g. "trip to Paris, February 2004". I then import the contents of this folder using iphoto and let it do it's strange cataloging business.
This is not ideal, as it is not as simply to do as simply plugging in the camera and clicking import. It is more like what I would expect to do on a PC, but at least it works and is safe. It also means I have 2 copies of all my photos (on 2 different disks which is good in case one fails.) I also have a copy of the files that I can use in other applications without upsetting iphoto and without having to export them from iphoto first.
I use iphoto for viewing, printing, publishing to homepage etc, but I like the fact that I can also see all the files in properly named folders that I am in control of! I would hate to ever have the scare again of thinking that I had lost all my photos.
Hope this is helpful or interesting. I'm sorry if it isn't!
Dobbin
PS. You can see some of my photos at
http://homepage.mac.com/robin.h if you'd like to. There are some gaps as I am currently updating it all.