I just played a basic run through Emerald Hill 1.
Clock Start Time - 1:59:49 AM, 2004/10/31
Flagpost Crossed - 1:00:14 AM, 2004/10/31
The run itself wasn't very good, but based on the official timing mechanism that monitored the game, it says I just completed Emerald Hill 1 with a new record of -3575 seconds, for a whopping 3595-second improvement off the existing record.
Let's see how long that record will hold.
UPDATE: As of the fifth Northern Hemisphere iteration of this challenge (2008/11/02), SonicAD and SpinDashMaster currently hold the record with -3578.