In my experience, the best thing to do is just set core=dynamic and cycles=max. That works for 99% of the programs I run. For the others, I just hit ctrl-F11 to lower the cycles.
I have a dedicated DOS directory with four subdirectories.
The first is COMMAND. In that folder I have all of the programs and BAT shortcuts I want: QBASIC, EDIT, FIND, PEDIT, XXCOPY, and a shortcut to Norton Commander- which I almost never use.
The second is the games folder.
The third and fourth are the NC and Qbasic program folders.
Every folder and subfolder has been renamed to work with 8.3 file names.
One of the more annoying parts of using Dosbox from the CLI is that you have to keep checking the names of the game executable. Usually by typing DIR /P.
I worked out a unique solution to this problem. Inside every game folder I created a batch file called RUN.BAT. The batch file has a single line with the name of the game file. So, for Betrayal at Krondor it would say "krondor".
So, when I want to play Betrayal at Krondor, for example, all I have to do is launch Dosbox and type
cd games/bak
run
Now the really cool part is that I have the entire DOS folder on a network share. So, from any of the computers on my network, all I have to type is
cd games/bak
run
Of course, this is done using network drives and the Dosbox autoexec.
All things considered, it is a neat and elegant system, and I am very proud of it.