Spirit just linked me to this thread. I'm the author of Noesis. Hi!
@sock, it imports multiple skins, but doesn't export at the moment. I can give you a commandline switch or something to import additional skin pages to stuff into the mdl export, if that's what you're looking for. Noesis also supports concatenating skeletal animations via commandline, but the only path for doing that sort of thing with vertex anims involves having to export to a modeling suite first. I can stick that on the todo as well.
As for your interface issues:
"Can't select/display multiple skins on models" - You can - Tools->Data viewer->Model #, then select the textures in the model to display them.
"Can't goto certain animation frames, only got fast forward and reverse." - You can do this too. Newer versions of Noesis have an animation slider, but just like textures as well, you can select them in the data viewer to display them.
"Each time I export the interface resets, it should remember each export file settings or allow a template/default to be setup." - If you want to do repeated exports with the same setup, I recommend the commandline using ?cmode. See the readme.txt for details on using console mode.
"I would love to export a batch of files but the command lines dialogue box does not work for me. When I specify parameters it ignores some of them, eventually I gave up trying because it did not make any sense." - I'm not sure what's going wrong for you here, I use commandline mode all the time. Can you give me the commandline you're trying to use, and the data you're trying to use it with?
Also, the Noesis page doesn't have a donate link, but my personal web site does. :)
http://www.richwhitehouse.com/index.php?content=inc_about.php
@ijed, Noesis will generally spit errors out when something goes wrong. If it isn't, something's gone really wrong. Can you send me the files you're working with and tell me what you're doing to make Noesis fail silently?
You can both send stuff as needed to the e-mail on the contact link. (from the richwhitehouse.com link above)