Number of indexed pages is shrinking

I would suggest you to perform the following checks, which I practice in case of such problems:

1. Check your robots.txt, if you accidentally disallow some directories on your website.
2. Check your page for presence of robots=noindex meta tag. Some seo-packs for CMS engines have this option enabled by default. Use it wisely.
3. Check your internal linking structure. It might be the case that some of your internal links to the problematic/disappeared webpages get broken (use Google Webmaster Tools for that).
4. Check your "description" meta tag on the problematic webpages. The text in this tag should vary from page to page. Google recently started throwing away pages with similar description fields (use Google Webmaster Tools to see pages with the same description field).
5. Check your pages for duplicate content. If you get a lot of duplicate or non-unique content, Google may apply site-wise penalty.
5.1. Some CMS engines have their internal by-default pages (forum, blogs, news, etc) which are not unique net-wise. If they accidentally get into index, Google might penalize the whole website to certain extend.
6. Improve your internal linking structure. The best approach currently are not sitemaps or extensive menu, but interlinking in the style of Wikipedia - the internal links are inside the content. Google love it!
7. Write and add some new and unique content for the problematic directories.
8. Get some backlinks to these problematic directories from trustworthy websites.
9. Finally, validate your html-code for serious bugs/mismatches of tags and for compliance with the standards.

Hope this helps.

Was that all unique content?
Also have you lost some of your backlinks recently?

I think you should check your content for duplicates on net.