You specify the 'name' you want for each game in the dat file. So you could easily just modify the cobracommand to be cobrac or ccommand or just ccdaphne. It doesn't matter to me. Daphne uses different names then mame. I actually used the mame names so I didn't have duplicates, but I thought all the duplicates where for the same game (since mame states that it works with a bunch of laserdisk games, but it doesn't).
I will take a look at update my default daphne.dat file I uploaded to make sure there are only the same name when they are the same driver.
And yes, you specify the order in which you want the games 'added' to the list. You add them based on which you want. For instance I want all the zinc games to run instead of the mame equivilates... why? because my arcade machine computer cant play any of them. But Zinc can. So I add all the mame games I want, then I add all the zinc games... They override the original mapping to the mame version of sfex2 to the zinc one. Only one sfex2 shows up in your list.
But you can add and remove games based on the emulator, or based on the other filters (from catlist/nplayers ect). So with a few lines of xml, you can remove all japanese majong games if you choose or move all mature games ect.
So for me... I have about 10 control panels for my arcade machine. I have one configuration (or emulator) for each one.
on my 2player 8way control panel, I add all mame games. Then I add all 8way with 6 buttons games, but with its own ctr directory (so I can change the default for buttons 1-3/4-6 swapped once). Then I remove all games that don't match the controls, then I removed all the language specific games if they are trivia games... Then I added all the zinc games, started using the AAE games (because they look a lot better on my arcade monitor).
Oh, and I use smartclones, so that I can get rid of all clones, but use a clone if mame is emulated better in the clone.
In the end, I have a listxml output of only the games that I want to play on that control panel.
I'm doing the same thing for each control panel I have... This allows me to use any frontend that handles multiple emulators (and seperates them) to handle multiple control panel... But as a side effect, it allowed me to play with 10 frontends without having to figure out how to handle multiple emulators in each frontend. When doing this, I changed the frontend that I chose on my arcade machine just out of chance. But some frontends can take months to tweak properly. But most can work very quickly with a single version of mame.
Anyway, this was just a tool for me. I thought it might be useful for others... The only options I added that I don't plan on using was the old listxml and the listinfo... but these both took me a total of 10 minutes to add... Never know, someone might be interested in them

Lilwolf, I've been following this one for a while, but it has me confused a little. What exactly does it do?
From what I understand it's making a big gamelist in the mame format and tricking the fe into thinking all the games are mame and I'm assuming there is an exe you put in place of mame that acts like a wrapper and launches the appropriate exe?
If that's the case then how are you going about the various conflict problems?
Example:
Badlands in daphne... the shooting game, has a rom name of badlands
Badlands in mame... the post apocalyptic racer, still has a rom name of badlands but it's a totally diferent game with different artwork.
The same goes with cobra command and a dozen or so titles I can vaguely remember having conflicts with.
Also of course there's the cps2/m2/whatever emulators that only emulate games that are already in mame. Of course I'm guessing they are the reason you made this, but does the app use a hierarchy to determine which one to use or what?