Parallax scrolling sites have started to go by the way-side thankfully. Like so many things on the web, when something new is discovered or introduced, designers and developers use the crap out of it and run it into the ground. It’s started to even out now and fade away a bit.
But some of the aftermath and learning that came from developing sites that predominantly live on a single page or two (and scroll a lot) still holds true.
The SEO-expertise site, Moz has a great article / collection of solutions and examples for maximizing the search engine optimization potential for long-scrolling sites (regardless of if/how that scrolling animates).
Source: Moz Parallax Scrolling Websites and SEO – A Collection of Solutions and Examples