My organization system is fairly simple: Animated Items first, then EIs, REIs, MCs, Cash-shop items, RIG items, event items, gold-shop items.
Within each item type section: AIs are organized by most used to least used; EIs, REIs, and MCs are organized by release date; Cash shop items are organized with favorites first; RIGs go from most to least expensive (approximately, they are grouped by price range mostly); event items aren't organized, because I only have a few in my main inventory (the rest are in storage), and gold shop items are organized by the order the tabs are in the dress up page, with sets together (all my different color elven circlets sit nicely in a row).
Woah, well after writing that all out it doesn't seem so simple anymore. sweatdrop
I tend to organize once a month, I usually have a new row of items by then to put in their place. Once you get a system set up its really easy to maintain, and you'll get used to where the items are really quickly - after I set my invo up it took no more than a week to reorient myself.
I wish you luck organizing your inventory! I know it can be a very daunting process, especially with the current really old inventory arranger (I think an update for that is planned for this year?).