After pretty much doing nothing else for the entire day I finally finished extracting all the models from Cyber Arena. The models are saved in the Collada .dae format (pretty much compatible with anything). They are not rigged, and it will probably take another few years until you can get bones out of 3ds formats anyway so this probably the best it's going to get. Textures with transparency have their alpha channel in the main texture image, you just need to apply it after importing.
On the technical side, I mentioned in another topic how some models could only be extracted partially depending on which version of the Appmon's model is used. In the end it turned out that the "Applink" model was pretty much guaranteed to work every time while the other two (normal and virus) only produced complete results in a few isolated cases. In order to remain consistent all models in this collection use the applink model; however sometimes despite being incomplete the normal model would contain some other assets belonging to teh appmon (one came witha bag, another one had a little gamepad for example) in those cases, if the asset had no missing polygons I would copy it over to the applink model to make things as complete as possible.
I think the reason why the applink model could be extracted but not the others had to do with the rigging of the model. The way rigs are saved in a file can be complex and it seems in this case not only is it impossible to get the rigging out of the file but the rigging actually interferes with the extraction causing the models to be corrupted. Because of this we are very lucky that the "applink" graphics work the way they do. The applink model is simply an identical copy of the appmon's normal model (In the cases in which there wasn't much missing from the normal one I could confirm that the geometry is exactly the same), but since the Applinked Appmon never moves (it just wobbles up and down a bit but the geometry isn't animated) it was saved in a static pose without any rigs. That's also an advantage in the sense that the posed models are nice to look at without the need to re-pose them from a potentially awkward T-pose. However on the other hand the fact that they don't come in said T-pose could make manually rigging them more fiddly than it would be otherwise.
The current number of Appmon models in Cyber Arena is 136. The in-game index goes up to 147 but those 11 additional appmon are not actually obtainable yet (they have folders, some scripts but no models).
Here is a list of all of them (all gaps have been filled in):
(Note that the ID of the model doesn not necessarily correspond to the Appmon's number in the in-game dictionary)