Hmm. I really like the idea for having seperate folders for this rather than adding another field with "Owned" as its flavor.
I do not like having comics I own listed along with comics that I do not own. I find it to be cumbersome when browsing. A display dependant on a filter by field value would remedy this if they were listed together, but your folder scheme would act as a sort of strain, while being both simpler and more intuitive (obvious). In contrast to what I imagine manifesting as your folder idea (which I am for, as stated above) there is the "other" way that comic software typically does this: they simply throw out long lists of comics, with a field that either has a "y" or "n" or "0" or "X" in it indicating whether a copy is owned. These "y"s are usually then swamped by "n"s, and it is typically a trial in patience simply to find what I am looking for, or to tell by a cursory look what I have and do not have. I believe ComicBase still does it this way. Collectorz.com uses a filtering system, but it is semi-annoying to me.
Anyway, I think the folder scheme(owned/not owned/wanted/missing/whatever you decide to label them) is consonant with the basic operating scenario that Comicster is based on (paradigm schmaradigm).
Then again, a field devoted to storing this value (of whether it is owned or not) would potentially be quite a bit more future proof. And this, surely, has to be taken into account.
It also occurs to me that if you include something along the lines of a field or folders for indicating the ownership status, you may then also become obligated to create another field for "#. of Copies", or something similar. A slippery slope towards database-ishness?