How did time machine back them up? Were they organized in folders at some point? Maybe you can go back and pull out that backup, preserving the folder structure you manually created.
If it just backed up the iPhoto library, then your best bet is to go to Pictures, and right click the "iPhoto Library". Find your pictures in there, and drag them out. Organize them yourself in folders, then delete what remains of the iPhoto library file as it is not corrupted.
Once all your photos are organized the way you want, open iPhoto (it will create a new library), set it to
not copy files when adding to the library, and drag the photos folder in.
It should then re-add everything, but not copy anything to the library. You have full manual control over the photos/folders. You would have to manually import things into iPhoto by dragging.
All this work is what makes me hate iPhoto. That and the fact that it completely disregards my organization and throws everything together. Sure it has cool thumbnail views but I found a way around that. Go into finder, select block or icon view, right click and select "view options"
I do these settings:
All Windows
Icon Size = 128 x 128 (the largest it will go in OS X 10.4 Tiger)
text size =12 point
Label Position: Bottom (so the thumbnails will organize properly)
Show item info enabled
show icon preview enabled (Icon preview is important to view photo thumbnails)
Keep arranged by: Name
Background: Black (but you can choose any color or photo.)
Now whenever I enter a photo folder, I select the icon view in finder, and I am shown a bunch of thumbnails which helps me preview images quickly without having to even open them.
Of course Leopard has coverflow which probably works better, but this method is the best I can do without having a third party app handle my photos.
edit: here's an example: