"The birth of a Paradroid" - Paradroid development journal for the C64 by Andrew Braybrook: http://www.zzap64.co.uk/zzap3/para_birth01.html
"Mental Procreation" - Morpheus development journal for the C64 by Andrew Braybrook: http://www.zzap64.co.uk/zzap23/mental1.html
"It's behind you" - R-Type Arcade conversion for the ZX Spectrum, free e-book by Bob Pape: http://bizzley.com/
Free sample pages of the development journals for Prince of Persia and Karateka by Jordan Mechner: http://www.jordanmechner.com/backstage/journals/
Prince of Persia code analysis after it got open-sourced in 2012; by Fabien Sanglard: http://fabiensanglard.net/prince_of_persia/
Analysis of Pacman; long after the fact: http://home.comcast.net/~jpittman2/pacman/pacmandossier.html
Any other? I'm sure there must be many nowadays...
Edit: Here it is (in 10 parts): http://popc64.blogspot.fr/2011/10/part-one-why-hell-would-an...
Edit: Here it is (in 10 parts): http://popc64.blogspot.fr/2011/10/part-one-why-hell-would-an...