I used to use Magic workstation (MWS)... but there are some bugs which killed my master library list and a whole ton of work, alas... so I decided to move to a paper/scan format... easy enough.
I use the DCI Deck Checklists to inventory my cards, scan them and have a web site to check on what I have/need while shopping in any store around the world... using an iphone, ipad, computer, et all.
Physically, cards each sleeved & organized by edition, by color, alphabetically. Contained within thirty or so 3,500 card boxes. Bulky, but there are not many ways around that, ha.
The promo collection, which is my present focus is not in boxes, but rather stored in 9 sleeve card-pages... I find it easier and more entertaining to thumb through these. *grin*
What does it look like online? Easy....
*My organization method does have some simple drawbacks = updating.
If I get a large update I
1. Write the changes down on the 'master piece of paper for that edition'
2. Scan it
3. Upload it
My biggest challenge right now is deciding on how to organize the darned promos. I think this web site has the best list, so have adopted it's categories. :)
Magic paraphernalia is more challenging - clothing, props, posters and oddities just have to sit on the shelves looking kinda organized. The 'Magic Room' is shared with my girl's sewing machine. :)