For SH3? There are several 'Supermods' that change everything. They are mostly devoted to either gameplay or graphics, or both. The best way to go is with one of the supermods. Which one you choose depends on what you want from the game.
Here is a comparison I made some years ago.
http://www.subsim.com/radioroom/show...30&postcount=3
As for smaller mods, there are literally hundreds of them. There is no top 10, or top 5. There are as many different mod combinations as there are players.
Here are some mods lists of some players. As far as my list goes, it changes almost every time I play, as I'm always trying out something new. If you have any questions about any of the mods, just ask them here.