The Duke Nukem 3D v0.99 beta is an early look at the shareware version of the game. It was leaked from a magazine previewer named Jim. You can see a message from George in an included text file. After this version was leaked, it is safe to say 3D Realms hasn't been sending out beta versions of games to magazines. There are some minor differences in this version, such as the message that rises up on the building in the E1L2 is different. It was hosted for a long time on Lon Matero's site, which is now dead, but a WayBackMachine archive exists.
Beta Compiled: Janurary 4, 1996 (1.0 released on Jan 29, 1996)
Note that all the files showcased are different on a byte for byte comparison. They may not have any visible or audible difference.