My Virtual Console collection has grown quite large, and I'm conflicted about how to organize them. I suppose I could just go alphabetically by system (NES A-Z, SNES A-Z, etc.). Another way I've thought about going is grouping series together, and then putting the games in the series in chronological order (SMB, SMB 2, SMB 3, SMW, SM64), but then I'm left over with the games that have only had one entry released on the VC.

So how do you guys organize your collection?

Very complexly. So complex that I can't even remember what the order was supposed to be...

I don't have many VC titles but I just put my favorites at the beginning.

Well all of my vc is in a folder and I put my vc in this order: nes, gb, gbc, gg. Its in no order as really but I like to put special games (like donkey kong original edition) in first.

i group each series together and the games that are solo i put at the end. but if you put some on an sd card i guess thats another story

On the Wii I usually sort them chronologically in order of system and then furthermore, alphabetically by title. Yet for some reason on the 3DS I've sorted them by franchise alphabetically and then from there by the release date of each individual game.

I never organized my Wii VC games, but I organize my 3DS VC games by what year they came out, and NES on one row, GB/GBC/GBC in the second row, then games from other systems like the Game Gear games in the third row.

EDIT: I have all my 3DS VC games in their own folder.

Order them by system by original release date.

When they were released in Japan

Definitly favorites in the beginning, but other than the Castlevania and Ninja Gaiden series being in order everything is just random. I like
sticking things next to each other that look good color-wise. I don't like having rows of black against black. Gotta break that funk up with some color!

I organize mine in oder of console in order of purchase, for example, I my first 3DS VC was a GBC game, so I put GBC games first in my list, then GB games and then GG.

On the Wii I never bought too many, but the ones I have, I ordered them by franchise and popularity.

favorites first and sorta by series like mine is
FF4TAY
FF4
Final Fantasy nes
castlevania
castlevania 3
SMRPG
mario party 2
mario kart 64
SMB3
super mario 64

By console, and then alphabetically within the console. Wiiware after the VC games.

I dont have many (mostly mario) so, I organize them by series and when they released. (ex: Super Mario Bros, Super Mario Bros. 2, Super Mario Bros. 3, Super Mario World, Super Mario 64)

I have made a program (WiiFolder V1.2) that allows me to organize the games on my computer. On the left side are the games stored on the computer's harddisk and on the right side are the games stored on an SD card that is currently inserted into the SD card slot of my PC. By simply clicking on the "Copy" button I can move games from the harddisk to the SD card and vice versa. Also in both views you can filter by "WiiWare", "Virtual Console", "Download Content", "Wii Channels", "Demos" etc., search for a game, change the sort order etc. (It's made with Microsoft Access 2000. Only a german version exists atm.)
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dont be afraid of castlevania 2

Mine are pretty complicated, they go roughly by how much I play that particular series, then by genre within that series, then in release order. But for games that I only have one game in (e.g Megaman and Metroid), I put them together roughly by genre, even though it makes no real sense (I put Super Metroid and Megaman 9 together because you shot things in 2D)

I just organize them by franchise, and then by the order they are released.

I group them by series first then console.

So the first page is a row of NES Mario games, a row of SNES Mario games then a row of N64 Mario games. Then the second page is a row of Zelda games at the top. First column is NES games, second is SNES games, then the third and fourth being N64 games. Third page is a Capcom page. Mega Man X and X2 come after Mega Man 9 and 10.

Its very common for me to rearrange games as I get more.

For 3DS, I have folders for each supported handheld/console. Then by year of release going by the year that appears when the game is highlighted. Multiple games that are released in the same year is up to me, so grouped by series where possible.

I didn't put much effort into organizing my games. They are sort of all sporadically just there. I know in my head where each game is.