soslo,
I tinkered with Daphne for a long time before I got it working the way I wanted it.
1. tried PC as emulator to run LNK files -- doesn't work in win98se
2. tried using BAT files. Mamewah would execute the batch file then resume in the background. When I would exit Daphne, the screensaver would already be active in Mamewah. Worse, if I chose to have music during the screensaver in Mamewah, Daphne would grind to a halt as Mamewah accessed my MP3 directory (even though I couldn't hear the music)
3. tried BAT files using :"Start /wait" to run the bat files. This forces Mamewah to wait until the batch file is finished executing. I got inconsistent results. Sometimes it would work, usually the game would only launch the first time then it wouldn't work.
4. Someone suggested Batchrun. That's what I use now. Since there are not that many games supported by Daphne, it's not that tedious to set up. For each game, I created a batchrun file that changed to the proper directory then ran daphne with all the commandline parameters I want for each game, then returned to Mamewah. (Batchrun can execute commands sequentially and wait until each is completed before it starts the next). So I use batchrun.exe as the emulator and run the files I create as the roms.
If I had to do this for 100 games or 1000 games, it wouldn't have been practical. But for a dozen games, not so bad.
good luck,
Rocky