I'd like to reiterate and emphasize what others have hit on with regards to cleaning the shank area. You'd be surprised how much this area can affect the taste of your tobacco. I consider this the bilge area of the pipe where all the crap collects [lol]. Moisture, tobacco, dirt, dottle, unknown substances, Waldo--this is where they all like to party. Things can get nasty down there.
Twist up a paper towel and go at the bowl post-smoking to keep the cake even, clean your stem, and purge the shank area with q-tips/a shank cleaner when you do your heavy cleaning routine. Rinse and repeat until the Q-tips are either clean or a very light brown color. Don't be too aggressive with the circumference where the tenon inserts, as this could lead to a loose fit.
In my experience, this will keep your pipe smoking nice and fresh.
The "Professor Treatment" mentioned above is as follows:
1. Fill bowl until slightly below the rim with salt; cotton balls work as well, and is preferred if you have spider lines in the chamber;
2. Take a medicine dropper and add your spirit of choice (I use Everclear) to the salt. 10-14 drops should do it, depending on the size of the bowl;
3. Leave sit overnight (at least 12 hours, in my opinion). The salt will be hard and crusty and, if the bowl was dirty, brownish in color. Empty the bowl, making sure you get all the salt out of the chamber. Swipe with a paper towel and give it some more time to finish drying.
4. Enjoy.
Hope this helps. Cheers.