Visual Simulation of Smoke
August 2001 - Ronald Fedkiw, Jos Stam, Henrik Wann Jensen
This article describes how the authors implemented their simulation algorithm. It explains both the theory and implementation, and also how they rendered the smoke with hardware and global illumination. A very good article, although quite heavy on the science. The algorithm gives very believable results.
Physically Based Modeling and Animation of Fire
2002 - Duc Nguyen, Ronald Fedkiw, Henrik Wann Jensen
This article describes a physically based model for simulating and rendering fire in 3D.
This article shows how to simulate fire in an easy way by using normal fluid simulation. It's doesn't explain the necessary fluid solver though, but it gives links to other papers that do.
Creating Fire in a Particle Editor
Feb, 2009 - Bulatov Evgeni
Explains how a particle fire effect can be created with Magic Particles. The explanation is detailed enough that this can probably be brought into other particle systems with similar capabilities.