Back in the day, I used to try to keep my hearthstone and any important quest items in my last bag, along with a few food and drink items. This way, I could just open my backpack and say, "Oh look, stuff I looted that I need to vendor." Now that I'm 60 and raiding, I've found that my bag slots are taken up with different types of situational items - a few trinkets, my Nature Resist gear for AQ40, my Fire Resist gear for BWL, and a couple of different weapons for whether I'm standing back and need buffs, or in the mix and need to do damage. Popping open bags and trying to find what's what became a bit of a chore, and so I started looking for tools that'd help me manage my inventory.
For whatever reason, I've found that I'm best at sorting my inventory and keeping it relatively clean when I'm using a mod that combines all my bags into one giant bag. I like placing my hearthstone and mount in the bottom left corner, my FR gear on the right, and leave a bunch of empty spaces at the top. This way I can easily see what needs to be sold, and what I need while traveling around Azeroth. Ahh, sweet order out of bitter chaos.
My journey from disorganized, I-can't-believe-I-just-accidentally-vendored-my-lighforge-helm buffoonery to serene at-one-with-my-loots-and-my-boots inventory nirvana was not one of instant success. I tried many, many mods before finally settling on Bagnon. Bagnon was great, had no dependencies, and didn't disagree with any other mods. Our time together was like a spring romance before the tornado season of WoW 2.0.1 hit. Since the patch, I've been forced to give up on Bagnon (which has now changed its name and look to vBagnon) and move to OneBag. I'm happy for now with my simple system of one bag with a bunch of slots, and simply grouping items by type and usability.
So how about you folks, do you prefer to use individual bags for certain types of items? How do you sort what to sell from what you need on you? How about those of you who have bags for your professions - have you found that these new bags help you stay more organized? What experiments have you tried, mods installed and then removed, all in the name of better inventory management?