The first answer would be that they must be indexed, however through experiments and tests we know that links that are not indexed still pass-on a certain amount of link juice to your website.  This makes absolute sense because Google/Yahoo would not want to show all their inbound linking data and info about a specific website. That would be much easier to manipulate. There is much information available that show a “portion” of the link wheel that supports any domain and the best average of backlinks.  No one is exactly sure unless you work at Google.

We know that Google does not show all of your backlinks in webmaster tools and will constantly re-evaluate, de-index and shift weights around on all your inbound links.  This will happen because a backlink gains more popularity or goes stale and is dropped from the SERPs, all sorts of different changes that happen constantly to the search engines “environment” of data.  There are a lot of opinions on how indexing vs. crawling of backlinks may differ.

Indexed Backlinks:

• In-bound links that are showing in Google webmaster tools, Yahoo Site Explorer and/or SEO software
• Links that are showing in Google would be considered highest value
• You know that your receiving maximum benefits from that backlink

Crawled Backlinks:

• Inbound links that have been pinged and crawled by search engine spiders
• Carry “some” weight, but no one is sure how much compared to indexed links
• Usually these links do not have much “content” associated with the link, more content (when relevant) is going to help improve the association and worth of a backlink pointing toward your main site

SEO Tips for Getting your Backlinks Indexed:

• Always Ping  – use Pingler.com, Feedshark, Pingfarm.com(mass list pings)
• Setup an RSS feed with all your backlinks in them so spiders can crawl the feed regularly
• Build a 2nd tier of backlinks pointing at your 1st tier links (2nd tier can be much worse quality)
• Bookmarking Demon/Xrumer/Scrapebox are excellent resources for building a variety of 2nd tier links to get your primary/high quality 1st tier backlinks indexed
• If you are setting 2nd tier backlinks that point at your 1st tier, quality is not that important and don’t worry if your 1st tier properties get sandboxed, they will still pass on the link.

Please understand that having one backlink is better than none!  Just make sure to keep your backlinks in good neighborhoods, try to associate relevance and unique content with every link you make.  Whether it’s a small relation like a business directory or geographically, just stay away from spam websites that will affect your trust and rank negatively.

If you are having trouble getting your web2.0 properties indexed, definitely focus on building an RSS for those that can be dripped pings consistently, then you need to look at starting and creating your 2nd tier links.

I would really recommend a tool like Bookmarking Demon or Scrapebox, you can blast thousands and thousands of blog comments, bookmark submissions, Pligg sites, etc so that your main links are picked up and also this will distribute more links to your main site down the chain.

This has really become the standard in the SEO industry recently, especially after Google’s algorithm changes which have made it much more difficult to use poor quality/junk backlinks to rank for your keywords.  It’s better to build lower quantity, high quality link properties and then build a foundation of linking toward those.

William