A good introduction to hashtags can be found at Twitter Fan WiKi. More background info on hashtags can also be found at FactoryCity .
Basically you need to follow the twitter user "hashtags" (they will then follow you back to get your hashtags in your tweets indexed). Then your tweets with hashtags should appear at hashtags.org.
Skimming trough the above mentioned web pages, I found some basic rules that one should follow when using hashtags:
- focus on your update first and add hashtags only if they add value to the tweet
- find out if the subject you're tweeting already has an established hashtag
- append no more than one to three hashtags
- rather append or prepend the hashtags to a tweet than using the hashtagged words in sentences