I don't have any good Castle mods yet so I like to store my swords, clubs, shields and any kind of armor I collect at Battlehorn Castle. Then when i feel like playing as a mage I store thing dealing with that at Frostcrag Spire since it's one of my favorite mage homes.

I tend to keep my stuff in one house, so I only have one place to go when I need to drop things off. I usually get Benirus Manor early on, then stay there until I can afford Rosethron Hall.

About the only stuff my char keeps is lots of pretty outfits and good quality arrows. Let's see,

Her house is in Bravil and she keeps some stuff there. She also has it rather nicely decorated with pretty things.
She has a locker at the Arcane University which is handy.
Her magic bag of holding is wonderful for stuff she doesn't want anyone to know about, empty grand/black soul gems she doesn't want getting filled by rats and items she wants to keep dry, like her journal.
Another little bag she carries, just to organize all the 0 weight junk she has.
Superian, her black mare, has some nice saddlebags, and she can carry as much as, well, a horse. :dance:

Arbourwatch in Chorrol. Or if im on the road, in my pants.

The clams beside the prison sewer

The handy Bag of Holding. It has so much stuff in it that it propably implodes into a black hole pretty soon :ahhh:

Normally in houses, but i can't decide which to use. I have an assassin character in both Thieves Guild and Dark Brotherhood, so should i use the Thieves Den, the Vile Lair, or just the inconspicuous waterfront shack? :unsure:

I like the Thieves Den. It's like being the mayor of your own little town! A castle out your back door and the most beautiful sunsets out your front door. Fireplace? Oh my yummy - half the place is on fire, all cozy and warm.

Other options to consider might be the Sanctuary or, if you have actually completed the TG, the Guildmaster's quarters in the Waterfront.

I start out with the IC Waterfront shack and then move into Dareloth's House in the IC Waterfront, once it becomes available.

I've been using a carry all mod so that I don't get over encumbered while I'm in the middle of a large dungeon. I've been so caught up with playing that I wasn't dropping things off at my places. But after I started having so much in my inventory I noticed that the menu was taking longer and longer to open up that I had to start letting go of things.

Depending on the character, I usually initially use either http://www.tesnexus.com/downloads/file.php?id=7675 or http://tesnexus.com/downloads/file.php?id=16362.

Haven't advanced past there on this install, but I might use the thieve's den once I have enough gold for all the upgrades.

Frostcrag spire is pretty much my home.

Virtually all of my characters store the stuff they actually use at the Waterfront Shack, just because it's convenient and centrally located.

Those so inclined turn Rosethorn Hall into something of a museum. That's where the really nice pieces to which they don't have a personal attachment end up.

And those who hang around long enough end up "retiring" to their favorite house, and all of their personal favorite items end up there. That varies by character, and includes both vanilla houses and mods.

I have nice weapons and armor in my houses all over the map. Other stuff I want to keep (like artifacts, rare stuff, and tons of jewelry and precious gems) I generally leave in the watefront shack in the Imperial City. It's kinda funny walking in to that small shack and seeing the piles of valuables unmatched in even the grandest of castles.

I use a dimensional home with a spell to teleport there and back to the spot I left off - so I can quickly drop off\pick up things when the inventory gets low or over weight (used to use a good feather ring to be able to carry everything but after awhile it gets to be a pretty long wait for the inventory menu to load so having a drop off location works better !)

This made me
I can picture it now. Clams with Flatspace technology...

Clams with Flatspace technology

that don't reset

To many other containers in Tamriel have those weird wormholes

I store them in a little and solitary house I've in the Jerall Mountains, north of http://www.uesp.net/wiki/Oblivion:Dragonclaw_Rock. I grew tired of all my chars living in fastuous castles, and decided with my last one that a cozy little house was enough for him.

I havent "started" using mods yet - although i will - so i most often use my favourite vanilla house, the one in chorrol.

Or if i have a thief/assassin character i use the one in bravil.

I was about to post that I don't store stuff, I sell it, but then I found a reason to do that. Top-level Marksman training requires you to have an Elven Bow, and at the level you want that you can't find anything less than Ebony or Glass, so there's one item I want to grab when I find it, and save for later. I opted to leave it on view in the IC shack as that's the place I most frequently pass through, and I'd forget where I left it if I didn't see fairly often.

I've been considering making a small mod to provide display storage for Rings and Amulets. I find I'm carrying a lot around that I don't use, and haven't sold (yet) because I'll get a better price after Mercantile Mastery, even though I know I'll have nothing to spend the gold on by then. Having some way to display them might make me store them instead of just carrying them.

It depends what race I am, my khajiits main home is leyawiin, but has bought and is renovating one in Bravil as well due to the borders.
But I store my gear in storage boxes in guild halls added with OOO if I can't afford an early house.

Just a note that you also need an Elven Cuirass for Master level Light Armor training.

However, you should be able to get both items even if you are past the point where they first become available, unless you are WAAAY past (like beyond mid 20s).

I keep all my stuff in the Bravil riverside shack from better cities or if I'm traveling I store stuff in my Riverhold house in Elsweyr.

THAT is the awesomest reply yet... although I was under the impression that clams regenerate their inventory (chance of a pearl) every 73 hours? I guess not?

In Benirus Manor

The Vile Lair for my assassin-like characters. The Thieves Den doesn't give much in the way of storage and is mostly there for utility.

So, the Skingrad House is my big "dump" point.