Why not do both? Make standard links with fully qualified, working URLs, and use Javascript to replace the links' normal behavior with AJAX. This is often called HIJAX [1], and it works just fine for normal users, disabled users, and crawlers alike.
You'll notice that when you click to our other pages the content slides in as though its all contained in the original page. But if you have JS disabled, they behave as independent pages. Google has indexed all the pages on the site separately[2], so we're getting the full SEO benefit while also maintaining user experience for our disabled customers. Its a win for everyone.
Ping me if you're having trouble, I'm happy to help.
Check out my company's homepage for an example: http://illuminatikarate.com/
You'll notice that when you click to our other pages the content slides in as though its all contained in the original page. But if you have JS disabled, they behave as independent pages. Google has indexed all the pages on the site separately[2], so we're getting the full SEO benefit while also maintaining user experience for our disabled customers. Its a win for everyone.
Ping me if you're having trouble, I'm happy to help.
[1] http://www.domscripting.com/blog/display/41
[2] http://www.google.com/search?q=site%3Ailluminatikarate.com