Keep in mind that using the link analysis tool at Google, or even Yahoo! isn't going to give you a full picture of the number of links coming in to your site. Google does not display all the links that they record in their index.
It used to be that AlltheWeb.com was one of the best places to check links, they had a very comprehensive listing, I used them quite a bit. Now that they display Yahoo! powered search results, that's gone by the wayside.
Optilink is one of the better tools I've seen for checking for incoming links, though in reality, it's also important to look at your log files. Incoming links are great and can boost your SE score, but you need to remember that building good links is also about building links that will send you traffic. Using your referral fields in your log files can help shed light on incoming links that you might otherwise miss.
For example, your company might be mentioned and linked in a news story that gets picked up on the wire. Suddenly you get an influx of traffic, but you have no idea why. Checking the referral logs might show that you had a large number of visitors from a specific URL. You can then go to that URL and see why you are being linked to. The logs are useful because they'll often show a new link months before Google or Yahoo! picks it up and shows it as an active link to your site.