Its impossible to pick the best 3!
Sorry
I like a mix, news, interviews with corporate users, interviews with developers, coding, kernels, filesystems, hacking, patching, patents, copyright legal, hardware reviews, book reviews, audio/visual media stuff, encoding, ripping, playing, transferring, transfoming, streaming.
Issue 29 (July 2002) - Patching the Kernel
Issue 31 (Sept 2002) - Linux goes to Hollywood
Issue 32 (Oct 2002) - Building Better Databases
Issue 36 (Jan 2003) - Optimise Your Linux Box
Issue 38 (Mar 2003) - You, Copyright and the Law
Issue 41 (June 2003) - Hammer Time!
Issue 42 (July 2003) - All About X
Issue 44 (Sept 2003) - Do More! 40 Pages of Tutorials
Issue 52 (Apr 2004) - Making Movies
Issue 57 (Sept 2004) - Faster Filesystems
Issue 58 (Oct 2004) - 58 Cool Hacks
Issue 64 (Mar 2005) - Stop paying for software
Issue 66 (May 2005) - Take back the Web with Firefox