Airdropping Comics
I am somewhat hopeful that ComicGlass or ComicZeal will adopt AirDrop, making transfers of comics from computers to iOS devices a simpler proposition.
At the moment, there are basically a few choices, all of which have some problems.
First Party Storage
If you buy an app like comiXology, you also buy your comics from them, and their company is the 'first party'. Assuming that company hosts the comic, then you are relying on first-party storage.
The best thing about this is that it's very simple, and very well integrated. You don't have to worry about servers, backups, changing formats, it's all taken care of for you, at least you hope.
The primary problem with this approach is the lack of control. Because the systems are well-integrated, they're often totally outside your control. You do not have the comic files themselves, they may or may not be DRM-protected, and you are heavily relying on the continued existence and co-operation of that first-party from then on. (There are potential problems with multiple devices and bandwidth and so forth, but those are secondary and fairly minor.)
If comixology were to shut its doors, be acquired or change their terms, your ability to access your comic collection acquired through them may be compromised. We've been living with DRM-protected server-based media empire long enough to see the potential problems with this.
I like comixology a reasonable amount, but I'm very wary of spending a lot of money with them and then hoping they stay alive, independent and with appropriate terms.
Second-Party Storage
You are the second party. If you buy a comic in digital form from a vendor that provides a DRM-free CBR (or you buy a paper comic and scan it, or acquire it in some other way), and you store the comic yourself than you're relying on second-party storage.
The primary advantage here is that it's all in your control. You can choose where to store your comics, you can give yourself remote access or not, you can back it up, or not. If formats change, you can convert them. You do not need to rely on someone else.
The primary disadvantage is that it's a real pain. You have to manage servers, you have to figure out how to get comics into your apps, you need to back them up or not, you need to convert them, or not. The integration here might not be strong, and it might not be what you want.
In particular, I find the transfer problem here to be a pain. ComicGlass and ComicZeal both support iTunes transfers, but I really don't like using iTunes to sync information, and so this has very little appeal. ComicGlass also supports HTTP Servers, if you want to set one up on your own machine to transfer comics to your devices, but maintaining an apache instance to serve up comics is also irritating.
Third-Party Storage
If the vendor doesn't store your comic and you don't store your comic, you can use some kind of third-party vendor. The most likely scenario here is someone like Dropbox or one of its may competitors. I'm going to use Dropbox as the representative case here.
This can only work if you get your comics from a source that gives you control, at which point you can store then on Dropbox either permanently or temporarily.
This hybrid approach means that you might not have to worry as much about servers, backups and so forth. Several of the comic applications support this kind of integration reasonably well, and it's less irritating than using iTunes (at least, to me).
But comic book archives aren't the smallest files in the world, and storing a large collection on something like Dropbox will cost you. Alternatively, you can use Dropbox as a transfer mechanism and delete the files after that, but the idea of sending files to California when the two devices are side by side is also somewhat irritating to me.
Enter AirDrop
I'm hoping that AirDrop will let me use second-party comic storage to give me control over the collection while still making the transfer part less painful than it currently is. It's still early days for AirDrop, so it might turn out that it's not a great solution for moving files between two devices, and that it's better suited for transferring files between users.
It's also possible that none of the comic-reading apps will adopt AirDrop in a timely fashion (particularly if it turns out not to be well-suited, but in either case).
Still, I'm crossing my fingers and hoping that AirDrop does turn out to be a good fit and that it makes this part of the process easier.