The Google Picasa OSX app is pretty nice like that, it doesn't interfere with your folder layout, so you can store your .jpegs just the way you want them, and i

The Google Picasa OSX app is pretty nice like that, it doesn't interfere with your folder layout, so you can store your .jpegs just the way you want them, and it will index them and let you browse them nicely. You can throw out the Picasa app and not lose much, your folders are still there with real actual files visible to Finder and the terminal. The only downside is that it looks very unmaintained these days. They haven't even added support for Retina graphics (in a photo viewing app!!!)