Google's John Mueller replied to a question around links found in JavaScript saying that once the link is rendered, Google will treat the link like how they treat any other link. John Mueller said ...

Google explains how to ensure links work properly with JavaScript in the first episode of the new Lightning Talks series.

So if you want your links to be found, be safe and put them in standard html format. But if you don't want your links to be found, putting them in JavaScript or Flash won't guarantee that.

Always test your pages using Google’s own tools and third-party resources to view the rendered HTML to make sure all your content is showing up.

I expect I’m not alone in that respect. My experience is that JavaScript-only content can take longer to get indexed compared to plain HTML.