As far as alternatives to basic stretching, there are many ways to try to treat your sore muscles.
The most common recommendation is to use a topical analgesic, like Ben Gay, but studies have shown that the active ingredients never reach your muscles. They are designed for arthritic pain, you should not be used for muscle soreness at all. Internal analgesics like Advil, Aleve, and Motrin can ease your pain, but they do not get rid of it any faster.
Icing has little efficacy for muscle soreness from running, and heating is the preferred method. No one really knows for sure why this is true. However, it is commonly thought that this is because the cells in your muscles need to remove the excess lactic acid from your body, and they cannot do their job if it is too cold for them to work. Lightly heating your muscles will help your cells do their job. My personal favorite method is the ThermaCare line of products that you can find at your local pharmacy, but there are other heating pads out there.
As I mentioned before, lightly heating your muscles is the best way of speeding up your recovery. As such, the best method is simple stretching and resting so that your muscles can recover. The "Marathon Stick" that someone else mentioned is an easy way of massaging your legs and many hard-core runners like to get professional massages after their races. I see no problem with either approaches since they lightly heat your muscles towards a speedier recovery, and they work!
Good luck on getting rid of your soreness.