This has been driving me mad as well.
Having finally got round to properly sorting and organsing everything in iPhoto (I've been scanning hundreds of old slides, so that's forced me to organise myself!), it's been infuriating to see Apple TV (Gen 3 if that makes a difference) display them in a very odd order - based, I think, as others have said, on "modified" date, over which I have no control.
My work around is to change the "Sort" order in iPhoto.
iPhoto is setup with a series of Folders (one per year) and, in each folder, a handful of Albums. There is always a "General" album for the year for most photos, plus one or two others for major holidays. So, for example, I'll have a 2012 Folder, and in it, Albums called "General 2012", "London 2012".
Makes sense to me anyway!
Within each Album, photos are sorted by date - if the date was not correct, or it makes sense to change the order, I've changed the date. Which is where it all goes awry for Apple TV.
What I've now done is to batch-change the "Title" - which reflects the Album name, and, when I do this, selecting the "Append a Number to each photo" tick box. So, the titles of each photo will be "London 2012 - 001", "London 2012 - 002" etc. I then change the "Sort Photos" order under the View menu to be "By Title" (it will have changed to "Manual" if you've moved photos around). Nothing changes in iPhoto, as that's the order they were in anyway, but Apple TV now displays them in the correct order.
This seems to be working.
I'll keep the date organised as well, as if that's wrong iPhoto slideshows go awry!
Hope that helps somebody,
Colin