1. Mike’s Free Link Popularity Check offers free, instant (no installing links to your site required.), online reports of a web page’s inbound links from other sites. It uses the top search engines; Google, Yahoo! Search and Bing (MSN)!
Thank you Mike, (whoever you are) for this handy tool!
2. The NeboWeb Inbound Link Tool will tell you instantly how many pages your site has indexed by Google.com.
3. Google has some great Webmaster Tools to help you monitor your site structure and places you need to correct errors etc. It tells you how many pages are indexed, and how many backlinks are to your site are things you should know. It’s a great measuring tool to see which pages are most popular, etc.
4. This guy has a nice collection of tools for checking links and link popularity:
Most are tools you have to download. Some are free, some are not. I haven’t tried all of them, but he has gotten some great feedback for posting them.