Googlebot is getting better and better at following javascript links, so I don't think javascript is a good way to keep Google from finding and following your links. You would probably be better off using a robots.txt file.
Stop me if you've heard this before, but I believe it's a myth that pages can "leak" pagerank by linking to other pages. Each page gets a certain amount of pagerank that it can choose to distribute to other pages, but that page won't lose pagerank by linking to other pages. That said, you still want to make sure that you distribute that pagerank to maximum effect.
Best thing to do is make sure that every page on your site links back to your homepage. This means that every page on your site will be sending some of its pagerank back to the homepage, which will help to make your homepage the highest pagerank page on your site.
One other thing: ideally, you want Google to index as many pages of your site as possible. Google seems to like big sites, and having more content indexed could help you rank better.
Hope I didn't just tell you a bunch of stuff you already know.
[edited typo]