Killing 1,000 enemies is easy. Unfortunately, thanks to a glitch in the PC version--a bug that no one bothered to fix--you have to kill all 1,000
in one sitting. You CANNOT quit the game. You can retry/restart a level, you can
quit a level, but you cannot exit the actual program.
With that thought in mind, let's move on to the most highly trafficked stages in the game. I've uploaded YouTube videos that can show you how to eliminate nearly all enemies in the highlighted levels, providing you have Super Sonic unlocked.
You can do most of these tricks without Super Sonic, but it's obviously much more difficult.