Right, so a clean install would involve plugging in the new disk, formatting it with disk utility (HFS+ Journaled using GUID partition map), and installing Snow Leopard on it for a clean install.
Then, you have two options to get your data on there:
1) Boot from the new clean system and use Migration Assistant to pull over all the apps and user settings from your old drive. (note: when you setup the new system, don't set the initial user account to be the same as your old computer, because then you won't be able to migrate it, as it will conflict. so make an "admin" or "test" account, then migrate everything over and you can logout and log back in as yourself and delete the test user account).
This way is easy, but in my opinion, you'd be better off cloning, because this is bringing over all your settings, apps, and user directory anyhow. So any clutter or junk or settings that slow things down a bit will come over too.
2) Boot from the new clean system, create a new account for yourself (with your actual name this time). Update to the latest Mac OS X, repair permissions, install all your apps and update them all to the latest versions, and repair permissions.
Next, go into each of the folders in your old home folder on your old drive (Desktop / Documents / Downloads / Movies / Music / etc...) and copy all the items from the individual folders into their new equivalents on the new disk.
It's also a good idea to boot into the old system and backup your safari bookmarks, address book, iCal, etc so you can easily import them into the new system. Or, if you have mobile me, you can just sync them up to the cloud, and then sync them back down to your new system.
The downsides to this method are time (spend a day doing this, especially if you're doing Adobe and Microsoft updates after install!), and you have to build all your settings back up again. The upside though is you know you have a perfectly clean system to work with - the speed boost is appreciable.
Any way you do it though (cloning, migrating, or copying), you will have you old system on the old disk there so you can always start again if you mess up. just don't touch any files on the old disk! (ie - don't move files over, copy them. good to have a backup!)
whew!
Lee Tom