Up until now only websites with their homepage in the root domain (example.com/home.html) and not a folder (example.com/site/home.html) could have Google site links.
This has recently changed, however, so now websites with their main pages in a folder can get Sitelinks too.
For example, Matt Cutts, Google’s Head of Web Spam, wrote that he deliberately left a holing page on his root domain (www.mattcutts.com/) even though his blog’s homepage was in the “blog” folder (www.mattcutts.com/blog/)
so that he would be able to tell once Google managed to work with websites with their main pages mainly in a subfoler, as with his own.
As you can see from the screen shot above, Google is now showing Sitelinks for his domain for the first time, suggesting that this is also the case for other websites too.
This Sitelink update could well have coincided with their recent introduction of horizontal Sitelinks a few days ago.