I just started reading comics a few years ago, and I've been snapping up back issues as often as possible to get clear on the history of the universes I'm reading. And nothing about that process pissed me off more than getting home from a back-issue sale to find out I already had almost every issue I'd just bought.
I tried making lists on my phone. They were always minimal, hopelessly out of date, and never complete. I tried logging them with different tools i found online. But when I got to the store, it was a PITA it look up a specific issue and see if I had it. So I just kept buying dupes. Finally I got tired of it.
So I started building an online collection app that uses the ComicVine API. It's really simple (no custom lists or anything), but that's the point. You sign up, log the issues you own, and mark any you particularly want. When you find something you're unsure you own, or you run across a great back-issue sale, you log in to the site from your phone, log in (directly, or with Facebook, Google, or Microsoft accounts), and see if you've got it. Done.
It's up and running now at http://comimics.com. Check it out, and hopefully it'll be helpful for you. If not, let me know why, maybe there's a feature I can add that will solve the problem. I'm already working on a few...most importantly, importing your collection data from other tools, so you don't have to repeat the work.