Is it possible to complete the game 100% without using mods?
This answer is for the PC version of the game. I don't know if it's also true for the console versions.
There is supposed to be one water tower in the game located at (18111,15326) which does not actually exist and 6 collectible items (3 weapon parts, 3 vehicle parts) which should be awarded at the completion of "Into The Den", but are not. This means that players are stuck at 99.95% completion.
The mod you're thinking of can be found [here].
As of today (7/4/12), there are no official patches that I'm aware of to fix this.