I'm looking for a photo viewer that would sync with multiple (sub)folders on my computer HD (some of which are not in my MyPhoto folder), and would have a feature to do a slideshow on the iPhone.
Have you considered Dropbox?
It allows for any folder structure you like, and has a decent photo viewing and slideshow capability. And it's free up to a certain size, although depending on the size of your library, you might need to pay.
It's great at a Ton of other things, too.