Thanks Fifth,
I finally found and used your guide in Troubleshooting to do just what you described. Making custom shortcuts is the way to go. I saved I even made shwoopy icons for each of the games from screenshot pictures using Any to Icon.
Edit:
Okay here it is. Hope the pictures come out okay.
1) First picture shows where I keep all my files:
DOSBox folder - place where DosBox is installed. You may have it somewhere else. I like to keep it here.
DOSBoxConf - will house all the different .conf files for the specific configs of each game. Again, you may like to keep them somewhere else.
DOSGames - Game file folders for my downloaded games.
[img=http://img301.imageshack.us/img301/1793/dosboxshortcut01zq8.th.jpg]
2) Using the dosbox.conf file as a template, I created a new .conf file to handle the game specific configurations. Here are the settings I use for Master of Magic. It runs less choppy if you set the core=dynamic. Remember to put the header shown in [] above the correct configs.
[img=http://img301.imageshack.us/img301/5255/dosboxshortcut04me6.th.jpg]
3) I named it after the game and put it in my DOSBoxConfs folder. I leave the dosbox.conf as it is. I also threw my shortcut icons in there.
[img=http://imageshack.us/thumbnmail.png]
4) Below is a picture of the autoexec portion of my regular DOSBox .conf. The regular dosbox.conf will handle the mounting of the virtual C drive to my C:\DOSGames folder as always. The new MOM.conf will handle the changing of the directory to MOM and the launching of the magic.exe like shown above in 2).
[IMG=http://img301.imageshack.us/img301/6407/dosboxshortcut05tn8.th.jpg]
5) I made a copy of the DOSBox shortcut. I changed the Target as shown. The original .conf first, then the MOM.conf on top of it. The optional '-noconsole' option starts DOSBox with showing the console.
[img=http://img301.imageshack.us/img301/4861/dosboxshortcut08yu7.th.jpg]
And for a finishing touch I took a screenshot picture and converted it to an icon using Any to Icon, a shareware program I found.