At base 180 speed, Deoxys is, by far I may add, the fastest non-uber Pokemon. Even most Pokemon wearing a Choice Scarf can't keep pace with it.
However, the honor of fastest non-legendary Pokemon goes to Ninjask at base 160.
Deoxys-S is with 180 base speed.
Ninjask is second
It has base 160 speed.
third would go to electrode with 140 speed.
Top 100 speed Pokemon: http://www.serebii.net/pokedex-dp/stat/speed.shtml