General statistical theory

1. Professor Michael Lavine's Introduction to Statistical Thought (extensive discussion of important ideas in statistical methodology with emphasis on the likelihood principle. Has very nice and useful comments on how implement thing in R)
   

Spatial Statistics

1. Professor Mark Kaiser's notes for Stat 506 (Spatial statistics for statistics majors, thus more theoretical than what we cover, but a very good reference)
   
2. Professor Richard Smith's notes for Environmental Statistics offered at UNC Chapel Hill (most useful for geostatistics)