Thanks guys, and many thanks wiggy for the updated file!
According to wikipedia, by comparing the games that use the accessories, these are the ones that can use more than one:
Mouse AND Super Scope:-Lamborghini American Challenge
-Lemmings 2: The Tribes
-Operation Thunderbolt
-T2: The Arcade Game
-Tin Star
Mouse AND Multitap-J.R.R. Tolkien's The Lord of the Rings: Vol. 1
-Pieces
-Vegas Stakes
There are no games that support the Super Scope AND Multitap, and thereby there are none that support all 3 at once. That being the case, I've set up the icons for any of the combinations that might arise.
So here it is:
SUPER NINTENDO FUSION TEMPLATE 2.0
Other than several minor adjustments and general organization of the template, there are now icons for Number of Players, the Super NES Mouse, Super Scope, and Multitap. The Mouse and Super Scope both have Required and Compatible options, like the N64 Expansion Pak on the N64 template. The Multitap has options for "Up to (3, 4, or 5) Players with Multitap", since there aren't any games that support more than 5 players. If the game uses Multitap, I'd suggest you select the maximum number of players for Multitap, and in the Number of Players section, put the highest number of players without Multitap (usually 2 I'd imagine).
The Super Scope and Multitap icons are in both the left slot and middle slot. If there's only one accessory used, I suggest using the middle slot version so there isn't an awkward gap between that and the Number of Players. Hopefully that gives all the options needed. Arranging the NES accessory icons will be complicated...

Added to first post. Enjoy!
EDIT: Also all of my covers are updated to 2.0!
Wiggy, if you get a chance sometime, could you make these 2 as vector icons? I still want to add icons to the Super Game Boy covers (and possibly a future Super Game Boy 2 cover).
Game Boy Cartridge and
Super Game Boy Controller.