io9 has collected a list of alien alphabets, including Marain from Banks’ The Culture books, Ancient from Stargate, and (of course) Klingon. They’ve also got links to fonts based on all of them, so now you can write your own secret messages in Kryptonese.
There are lots of other alphabets and fonts they don’t mention in their article. A few others are listed below:
Not SF, but Peter Klaasen has a collection of Tolkien fonts.
The Alien Nation Appreciation Society has the Tenctonese font available (near the bottom of the page).