You can make comics in flash, just flash is more known for animations. And the VGcats dude actually uses flash for drawing, but exports images.
Still, nothing stopping someone from using or abusing a different program to make a comic (Real Life comics uses adobe illustrator) like inkscape or some animation program and just taking snapshots. (Poser-like appications)
What I'd rather not see and not encourage people to do is "screencap" comics. They fall into two categories. The first being intentional use of 3D software to give the look and feel of a 2D/3D game/movie, and taking snapshots to set it up like a comic, this is generally ok, but it requires a lot of skill to make it work. The other one is the intentional use of games like Warcraft, Final Fantasy, taking screencaps and maybe adding comic style dialog bubbles. This latter category is copyright infringement and frowned upon.
But I digress. The problem is originality with the use of software to generate things (including flash), as one usually is accused of ripping off another person who also used the same product due to use of the same library objects being used and slightly altered if that. This is why I mention "poser" explicitly because it comes with easily identified stock models. Flash on the other hand doesn't come with stock models, but there are a lot of stock objects available on the internet that are easily identifed as well.
So "Outstanding Use of the Medium category" would suggest use or abuse of a product to produce a webcomic. Like, a comic that changes everytime you read it would be a use the web(server) or html to give that effect.