There's a nice ongoing thread at forums.digitalpoint.com about getting more pages indexed at MSN.

Based on people's experience so far, it seems that MSN is not fond of deep Crawling.

One solution is to make a sitemap and link that sitemap to your home page. That will bring your pages to about 2 hops/levels from your main page.

Note that if you have more than a hundred links, it is better to separate it into a couple of pages all linked to the sitemap. Having 200 links in one web page is not a good idea.

It also helps to get some links directly to your sitemap instead of the main page.