The big problem, as I see it, is that webcam hailing between ships is a request that is limited to a VERY small subset of the player base. It would be more accessible to more people if there were options for audio-only interaction, or video files that could be used by a GM to create more immersion in a script.
As other people have suggested, the best solution would probably not be for Thom to implement a video chat solution, but to implement an interface or "hooks" that would allow players to use their own equipment and software to overlay a video or image over the Mainscreen, and pipe audio into the main speakers. Then you don't have to make Artemis invisible or use separate keyboards to give Comms control over the video input. All Comms has to do is activate a control on his normal console, and Artemis will switch to the video feed. (either by going invisible, or for full effect actually capturing the video input and displaying it to the screen, possibly limiting the apps that can be used)
For greatest functionality and applicability to the largest number of people, I would prefer the following:
1) A built-in text chat, using an extension of the GM interface. This wouldn't require any external mics or webcams, but is a good place to start.
2) The ability for Comms to display a still image on the screen, while playing script audio. This will attract the other players' attention to the screen, and serve as a way to identify who is talking. Artemis will provide a number of stock images, such as "TSN Command", insignia for the various enemy races, or a civilian starbase, and others can be created by the script writers and used in their scripts. As noted below, this image could be displayed over the Mainscreen view or in a corner, as in picture-in-picture. A full screen option should still be available, though, for talented script writers who want to show a still of the enemy captain, or even a fake "low scan rate" video.
3) The ability for Comms to play a video on the screen, with built-in audio. This can be in a standard format such as AVI, or OGG video for consistency. As above, this would be used by script writers for NPCs in missions, and would typically be activated by a button just like the one to listen to a scripted audio message.
4) The ability to pipe audio input, typically from the Comms' chat input, into the Mainscreen speakers. This lets everyone listen in to Comms chatter. This can also activate a mic used by the Captain, if equipped. A standard image should appear in the screen, such as "AUDIO ONLY", although the image could be overlaid over the Mainscreen view. (i.e., in a corner out of the way) Captains could also provide logos for their ships, or an avatar of some sort, which would be specified to Artemis in some way. (As an example, the images could be called shiplogo.00x, where x is the slot number of their ship. The Comms officer would still have to choose between the images in some way)
5) Full "on screen" webcam ability, where the Comms officer reacts to a request on the chat channel, and "opens up" the video channel for direct communication between ships, or the GM and any helpers acting as NPCs.
This list builds on the previous features, and could be implemented in order, giving Thom plenty of time to work on them. The interface for 2) and 3) already exists, and while 1) doesn't yet exist, it should be easy to add a "Send Comms" button to Comms similar to the one on the GM screen, and it could communicate back to the GM, as well as to other ships. I see the interface for 4) and 5) being an extension of the standard Mainscreen Controls, which Comms once had access to, but doesn't any more. I'd give Comms that access again, perhaps on the screen brought up by the "Send Comms" button. (Meaning Comms has secondary access to the Mainscreen, and primary access for incoming communications)
This latter idea could solve the issue of choosing between the images. Thom can provide standard logos for the ships, Artemis, Hera, and so on, and whichever Comms has selected on the "Send Comms" screen is shown as the overlay when Comms opens audio or video to the Mainscreen.