I have a somewhat organize system for new comics. I bag and board them as soon as I get them home. Then I sort them into two piles. One pile is major titles that I need to read before the podcast I do on Fridays, and the other pile are the titles that I can read over the few days after that. Once I read them, I turn them upside down on my nightstand, so I know what I have and haven't read. Once I have read them all, I enter them into my online collection on Comics Price Guide. For now, after that, they go into piles in my unfinished, unorganized comic room.
Right now I'm in the process of organizing my long boxes alphabetically, which has proved to be a daunting task. Eventually the plan is to have them all done, so that each week I can put my stack of comics from the week into their appropriate spots, and not let it build up like I did.
And I know we've discussed it elsewhere, but I'm super anal about cataloging everything now. So far I have catalogued a little over 4,500 comics, so being able to access what I have online is a necessity. When I'm at the come shop, I can pull up my collection on my iPhone to check it I need any issues.
Right now I also have a long box of back issues that I am ready to read, so I will typically take a small stack out to read after I've finished the current weeks books.
I'm the same as Chris when it comes to back issues, though. I can't read them until I have a solid run to read. So as my collection gets more complete, those books make it into the longbox I have marked "Not Yet Read."
Um, I guess that's it. It might seem convoluted, but it makes sense to me when I'm actually doing it all each week.