What TMC said...
If I had 3000 cigars I would do a wall in my office with multiple compartments glass front, separate humidity controls, roller sliding drawers at the bottom for boxes, rolling shelves in the middle for loose, Glass interior doors for those that need extra protection and alarms all over.
As TMC said, one section for those you go to often and one or two sections for those you do not want disturbed. I think I would also add Led Lighting, Ultra Violet lighting to keep mold and germs down.
I would do as much glass as possible so I could see the wonderful collection of boxes and loose, and keep the ugly boxes in the drawers. I would also probably make a shelf where I would have special spot lights softly highlight things like Opus XXX God of Fire, and my Cohiba 7x54 CC and whatever super cigar I was proud of.
In the back wall I would have a glass panel so that I could sit a mural behind my entire collection of scenes from the Plantations, and in the center shelf with my daily blends, I would try and get a collage of all my BOTLS so I can salute them as I enjoy a smoke.
I learned from the Native Americans to thank the animals that gave their lives so I can eat. I remember to thank Arturo, and Carlito, and Nick, and all the others who have been through so much in their lives so I can have a hour of pleasure once and a while.
Sooo I think if I had 3000 cigars, it would look like a museum, not just a humidor, and it would be the highlight of the room, and not just a piece of furniture for in its body lies a treasure of sacrifice and sweat and dedication that is too important to forget.