I'd recommend using Goodtools to rename your gameboy roms. You may also be able to use it to zip them all up? I know that you can use Goodwindows and the zip plugin to read zip files using goodtools, but I can't remember if it will actually zip them up for you? Anyway, you are best off to have them all in .zip format as then you can have a list in mamewah which is a mix of gba, gbmono etc..
There shouldn't be too much of a difference between the SDL command line version and the modified GUI version of VBA. The modified GUI version is just the full version which has the exit key mapped to escape. Baz created this one as it is easier to config the keys (ie you can just use the built in gui rather than having to work out numeric values and enter them in the config file) and allows you to use a joystick (I think?).
What should the ROM names look like? I have ROM names like "Dexter's lab - Deesaster strikes.gba" and some like "spyk3d.gba". I would like to see the list show "Dexter's lab - Deesaster strikes" and "Spy Kids 3D - Game Over" on the mamewah game list. In the tutorial on your web page you set the list generation method to 0, which I believe is "list of files names is the list of ROMs", so this makes me think the ROMs need to be named using their "long" name right?
The other issue I have to is to match screenshots and box art from your site to the ROM names. I believe that mamewah will requires them to match exactly in order to display them, so that means that all ROMs and artwork need to be named using the "long" name (i.e. "Spy Kids 3D - Game Over.xxx" rather than spyk3d.xxx", where xxx is zip and png). You suggest using GoodTools to rename files, I have no experience with GoodTools and will look into it, however I don't really like the idea of having the GoodTools tags like (U) appear in my mamewah list. The screenshot in the tutorial on your web site shows those tags.
Is there any way to get what I want (are there .dat files out there similar to mame's that will match names and "short" rom names?).
Edit: OK GoodTools appears to have more of a brain than I thought, it seems to use some kind of DAT file like is available for MAME (Edit again: err, I think, I'm so confused!

Any help on how to use the goodtools will be appreciated). Does that mean that Mamewah can parse that DAT file for list generation and therefore get rid of the goodtools tags for display purpose even though the files have the tags?