I had a big clearout not long ago and got rid of all my old/damaged/broken/unwanted toys which means that almost all of mine are in my top drawer in individual bags
I managed to slim down my storage not too long ago. All of my storage is based on how much I want to use things. For instance, the bedside cabinet toys are all small things that are quiet that I can use on the fly. My wand and bondage are in locked cases under the bed because i'm only going to use them when the house is empty or i'm with someone. The main collection holds things inbetween.
Used to have
My main storage box, which is a wooden box I stained and painted up with a lock attached to it - holds the bulk of my collection. There were two further boxes in there also which holds my lelo tickler and my mini floggers, and a Jejoue box which held other aneros toys, a cock ring and a pair of nipple suckers.
An Njoy box in my bedside drawer with a few aneros toys, a couple of rechargable bullets and a lelo liv, plus a mini bottle of lube
A small lelo box in my bedside drawer with condoms.
My bedside cabinet, which had lube and massage oils/candles (still there)
A larger lelo box which held a single feather tickler (didn't want it crushed)
A small lockable briefcase that fit into a drawer held my bondage stuff
Same drawer held all my chargers (Rakes of the buggers)
Two larger versions of that briefcase under my bed, one holding my wand and old packaging (And a couple of toys I didn't use.) and the other had the Monogamy board game in it.
Now, my bondage toys are all in the briefcase with Monogamy so that's gone from my drawer, My condoms went from the Lelo box to the smaller Salsa charger box. That lelo box now holds what used to be in the Njoy box, minus the Liv, which is in main storage. Chargers got slimmed down. Any duplicates went in with the wand, what was in with the wand was chucked. The feather ticker was liberated from the lelo box and went in with the bondage. The jejoue box was taken from main storage and emptied. All other packaging i'd kept hold off was dumped.
A good number of my toys are in the toy bags they came with or came with other toys, a couple are in lovehoney drawstrings and the rest are wrapped up in white cotton hankies or naked. My purewand is in a really lovely thick drawstring bag that I got on sale from lovehoney ages ago.
So now everything other than a couple chargers is in my bedside cabinet or under my bed. Much easier to keep track off. ^^ There is enough room left in my main storage that when it comes time to move I can probably squeeze in everything other than monogamy, so that hopefully wont cause any issues with people wondering what's inside the massive number of locked cases.
In lovehoney satin bags and in my bedside cabinet.
Don't you just keep them in your box?
...I mean their box?
Well... I think we need to upgrade to something like this now, been searching high and low for a big cheap wooden box and think I've found it:
https://www.homebase.co.uk/webapp/wcs/stores/servlet/ProductDisplay?langId=110&storeId=10151&partNumber=585235
I have one of the bigger LH delivery boxes under my slider drawer bed. Some of the cheaper toys packaging boxes(mainly the plastic ones) have been thrown out, ie cut into very fine pieces and stuffed in crisp packets so my parents can't see them!!
My Lelo toys are still in their fine boxes as are both sets of kegal balls. My 50 shades wand is also in it's fab box.
The rest of the toys are either in the pouches that come with the product or the LH satin bags. I've only got two of these bags, so when I add a new toy that comes without one a clean sock will do just the job to keep the toys melting together!
All my toys live in the big box. My current lube is in the same box, but I have a smaller LH delivery box with flavoured lubes and my least favourite toys that I don't use.
My brother has stolen the rest of the delivery boxes I've had to use tosteady his drum kit in the attic - completely unaware of what lay within the flatpacked cardboard! :D
The expensive/larger items we keep in their original packaging. The rest we keep in the Lovehoney satin pouches, all of which are kept in a posh box under the bed. It's getting to the point where we need to upgrade to a filing cabinet to store them all in soon!
Bedroom drawer expecially for them with lots of wine bottle bags, organza ones are the right size, no I don't drink either.
Mine used to live in a metal box in the wardrobe. But, having packed up my life and spent most of the past year living out of suitcases, they are currently in ziplock bags. Some here with me and some in a suitcase at a friend's place. One of the many things I'm looking forward to when I get settled somewhere again is being able to store things properly.
I've got a couple of pretty patterned storage boxes that I use for toys, lubes and lingerie, stacked on top of one another in the corner of the bedroom. They're cardboard but with a kind of shiny laminate coating on them so they're easy to keep clean, and they're each about the size of two large shoe boxes put together. Toys are kept within the box, but also either in their original packaging if it's not too big, or in a drawstring bag, just to keep them from contacting each other. No need to hide them since it's just me and the OH here, no risk of anybody going through our stuff.
I put them all in the box that I keep in my closet. 
I found that old dvd racks are perfect for toy storage, as plastics and such like fresh air:
http://img163.imageshack.us/img163/7341/toyshelves.jpg
1 drawer, 1 large tool box, 1 small tool box and another large box in a cupboard. 
I don't have enough room to keep everything in their boxes so I bought a mixed lot of cotton and silky drawstring bags and keep everything separate in those. The big ones live in the drawer under my bed, the little ones in a compartment in my chest of drawers, and the less-used ones in a little toolbox with a lock on, and my ropes and bondage things get bagged up as well and then kept in a drawstring gym bag.
Well I have sorted my collection and have a bedside drawer dedicated to my to-hand toys (my Lelo toys and Happy Rabbit, and various dildos) as these are quiet and needed a lot!
I also have three Medium LH Gift Boxes in a cupboard which are full of rabbits, my magic wand and other louder toys which make appearances less often. They are easy to get to though when needed, and most are stored in LH satin bags unless I liked the packaging.
In a draw under the bed. Easy to hand
I have mine in a box and i keep the packaging (if it's decent enough) to store my toys and keep them seperate.
Currently in a large black storage box like this http://www.ikea.com/gb/en/images/products/kassett-box-with-lid__0141911_PE301875_S4.JPG
Inside the main box I either keep the packaging with the item, or store things separately in LH drawstring bags (I cannot recommend those highly enough)
I use a box like this http://www.amazon.co.uk/gp/product/B0016ZGBRY/ref=oh_details_o05_s01_i00?ie=UTF8&psc=1 for my smaller items, dildos, handcuffs, lube ect it has a lock in the top, so that way I know the kids aren't able to get in it, and I can leave it down the side of my bed.
I can also take it to hotels ect as it just looks like a makeup / hairdressing box. I love it.
Little strummer boy that sounds great. :) I need a place to put my toys at the moment they are in a black plastic box but I want something with a lock on it ;)