Xenharmonikôn The first publication on alternate tunings I knew about.
The Just Intonation Network publishes a magazine called "1/1" advocating just intonation tunings for instruments. If you don't know what that means, they have put online an explanation entitled:"What is Just Intonation?" The Southeast Just Intonation Center has another, shorter note on the same topic.
Another publication is Experimental Musical Instruments, a quarterly magazine that often includes information about instruments that play in non-standard tunings.
Frog Peak Music is a publisher/distributor of materials related to experimental music, including alternate tunings. They are the distributors for Xenharmonikôn.
microMegas is an online microtonality revue.
This is where you can go for a Tuning & Temperament Bibliography
This is where you can go for a List of microtonal music on CD
The Richter Herf-Institut of Research on Musical Basesis an Austrian research institute with interests in tuning.
The Southeast Just Intonation Center is a nonprofit cultural and educational organization. Its purpose is to provide an environment and facilities in which musical activities oriented toward just intonation may take place.