What I've come across here is that there are really 2 different animals - there are stickers and rub ons, which are pretty uniform in size and stackability, and then 3-D letters (metals, chipboard, etc) which really have to be stored in a different manner. Because you're not going to be able to cram a can of KI Soup alphas in a filing cabinet with your Thickers. It just isn't going to work very well.
So let's see HOW to store the alphas first (both categories can work here). You can sort by color - which I find the easiest method for stickers/rub ons. You can sort by material type - which may be the way to go with the 3D alphas. You can sort by manufacturer. Or you can sort by letter for the 3D alphas. It's really up to you and the way you scrap. Systems can be mixed and matched as well - all my sticker and rub on alphas are stored by color, my "sets" of 3D alphas are stored by color, and the remaining 3D alphas are stored by letter. It works for me!
So WHERE to store your alphas? Let's tackle stickers/rub ons first. To me, any alpha set that is attached to a flat sheet is a sticker. So the Basic Grey chipboard sheets are stickers in my book - even though they are made of chipboard. If I can't easily remove them to store on their own, then it's a sticker. So here is my mega-list of links, please check them out and see if you can find a solution that will work for you and your space. Please note that the links I posted are intended to give you a visual idea of what it is I'm talking about - it doesn't mean I endorse the product or the store.
Clip-It-Up: http://www.clipitup.com/ They have the original, plus some new variations released at CHA. One of the best tips, tho - if you Google "homemade clip it up" you will find hundreds, if not thousands, of web pages from crafty scrapbookers who have devised their own systems, from spinning racks to wall-mounted rods. If you like things hanging from hooks, where you can see your entire stash, this is a great solution. You can also use rings instead of clip hooks, I love this solution: http://pinkpaislee.wordpress.com/2009/03/16/alphabet-storage/ and this one too: http://outtathisfunk.blogspot.com/2008/01/sticker-gripper.html
3-ring notebook or a Crop-In-Style Paper/Sticker Binder: http://store.scrapbook.com/psbbinblac.html
Vertical paper or magazine holders
On hooks in pegboard or slatwall
12x12 multi-drawer chests: http://www.stacksandstacks.com/iris-3-drawer-tabletop-plastic-chest/
Expandable files - great for crops!
Hanging file folders in a rolling cart or a file drawer
Stacked in a bin, basket or box - this works great for the "books" of alphas, like Making Memories rub ons
Cropper Hopper divided storage box: http://www.cropperhopper.com/dividedstoragebox-7x10.aspx
For 3D alphas, you need to figure out how you want to store your alphas - by color, set, letter, material. This will help you decide on what kind of storage you need and what size. Options include:
Zip top bags on clip it ups
Small jars in 3-drawer chests
Hardware cabinets: http://hand-tools.hardwarestore.com/70-420-storage-cabinets-small/storage-cabinet-603483.aspx?utm_source=nextag&utm_medium=cpc&utm_term=603483&utm_campaign=nextag
In bags in photo boxes
Tilt bins: http://www.amazon.com/gp/product/B000J07R8E
Floss organizers: http://www.amazon.com/Floss-Caddy-Compartment-7-x10-1-x1-1/dp/B000ZDME1A/ref=sr_1_3?ie=UTF8&s=home-garden&qid=1244335028&sr=1-3
IKEA Fira drawers: http://www.ikea.com/us/en/catalog/products/80073304
Muffin tins - this one is for buttons, but I've seen alphas organized by letter this way too: http://www.flickr.com/photos/wychbury/3193942747/
Spice jars or open bowls
Zip N Flip: http://store.scrapbooking-warehouse.com/278904.htm
Labeled envelopes - I've seen these glued to an address book by letter as well, but I think it could get bulky pretty fast
So now you know some options, here are the systems I found that worked for me.
I have a serious addiction to letter stickers (to the point that I really should have an intervention). I have found a working solution tho - I have 2 file drawers dedicated to stickers and rub ons. These hold all my non-book style alphas - I have them behind plastic divider tabs, sorted by color:
For my multi-colored alphas (meaning there are multiple colors on the alphas themselves or on the sheets), I ran out of room in my file drawers (oops!) and started stacking them in nice baskets (purchased at Hobby Lobby) on my shelf:
I also keep any insanely-large monograms up on the shelf there as well.
For my booklets of rub ons (this does NOT include my AC Mini Marks, I think those are flat enough to go in my file drawers), I found this beautiful carved wooden planter in the garden section of Hobby Lobby in their summer clearance:
So those are my sticker/rub on solutions. For my 3D alphas, I sort first by set. If they come in a complete matching color and font set (like Chip Chatter or the Making Memories tiles), then I put the sets into zip top baggies (jewelry section of Hobby Lobby) and store the baggies by color in cheap photo boxes:
Each box holds one color, so I can grab it fast and not have to sort through it. These are also great kid-proof options - my baby loved teething on these bags! Then it got to the point where I'd come in the room and find 7-8 boxes opened, baggies everywhere - they're now taped shut with 2 short pieces of masking tape. He can't budge it, and I just need to remove one piece of tape to flip open the top.
Now, for my alphas that either aren't in sets (like most of the KI lines (with the exception of the Soups), which have the same font but the patterns don't match at all), or my naked chipboard, I divide those up by letter. I started with the hardware bin about 15 years ago, then moved on to the IKEA Fira drawers about 7 years ago, and in my new space have the Crop-In-Style type cubes (from Target). Simply because I needed the room!
Each alpha has it's own drawer. All types of materials are mixed in here.
I would advise against breaking up sets if you submit layouts for publishing a lot - unless you have a really good memory of what's what.