Thanks, I appreciate all the suggestions. I think that for the purposes of this list, separating the full-size headphones into subcategories would be counterproductive to compiling a list of flagships by manufacturer.
We could go open, closed, circumaural, supra-aural, studio monitors, DJ, portable, etc. but as far as flagships go my criteria was to just show a representative sampling of each manufacturer's "top of the line" in totality rather than in each sub-category.
In the case of AKG, I think that many are awaiting a new flagship and the consensus seems to be that while the K701/2 scale up quite nicely, they are not in the same class as the K1000. There is considerable speculation as to whether or not Harmon is even willing to come out with a flagship replacement under the AKG brand. So the consensus seems to be that they are without a current flagship.
In the case of Beyerdynamic, the DT48 may be their best current studio monitor, but not their best headphone from what I have read so it's not their flagship.
I didn't even like separating IEMs into universal and customs, but in the case of many customs makers that make both I didn't see any way around it.
I think that we may still be missing a few manufacturers though, for example in custom IEMs the Starkey Tunz line looks like it needs some research, along with the Livewires offerings. Another example could be certain audio equipment manufacturers that have left the market but at one time had a legitimate flagship headphone in the marketplace, like Yamaha(?), or perhaps a company that is not even in existence anymore.
Anyways these are my thoughts. If you guys think it's worth expanding into something more I could try to accommodate that but I have some worries that it could get a bit messy or contentious.
Conversely, I am also open to turning the OP into a wiki and let everybody contribute, so if you think this worth pursuing please continue to let me know your thoughts.