A while ago we decided on a new method of timing runs (for GCN, PS2, etc., not handheld), which was to start the timer after the cutscene with bits and pieces from the actual movie, so as to A: level the playing field for all consoles, since some versions can skip the cutscene and others can't, and B: to avoid copyright issues, especially when uploading vods to youtube or anything like that. After testing it for like 0.2 seconds I figured out what's probably the best way for everyone to start their runs from now on. I do it here:

Basically you need to set up a save file (call it whatever you want), modify your settings the way you want to beforehand, press "Play," sit through the cutscene, and once you can pause the game during "The Venture," save and quit. Now you can reopen the save file, hit "Play," and have the stage select screen appear. Start the timer when you select "The Venture." This adds maybe a second over the previous timing of just waiting for the loading screen to start, so the difference is marginal, but I think this is a more consistent way of starting runs anyway. The idea came from my newly found knowledge of Super Metroid doing something similar for their runs, to skip an opening cutscene at the beginning of the game. With this, you can completely bypass that stupid movie cutscene (I mean it's a fun watch, but it's literally unnecessary), avoid copyright issues, save time, and as long as you never save during the run, keep reusing the same file without creating a new one and changing your settings over and over. :)