You can get a nice boost by running your Mac mini from a large, fast, external Firewire drive instead of the slow, puny internal drive. Or you could go one step further and get even better performace by going the hacker route deftly detailed by Arthur Whalem for the Arizona Macintosh Users Group (AMUG).
Using a $23 IDE adapter you can connect a 3.5-inch drive internally (replacing the 2.5-inch drive completely) and get around the space constraints by housing the drive externally. Believe me, it sounds more complicated then it actually is and Arthur does a fine job of documenting the process and the results.
Using Arthur's method, you will gain a significant increase in performance for a very reasonable price. If you try this at home - or you've already done it - let us know how it's working out for you!