If anyone ever used the Underground Hideout in Fallout 3 they might know what I'm looking for.

I'd like to find a house mod that has of course, upgrades you can buy, but also special items like alchemy sorters, enchanting/spellmaking stations of course, display/trophy storage, guest room(s), weapon display, mannequins, etc.

Basically all the fluff. Any ideas on the best house mod for this?

I'm not much of a house user, but http://www.oblivionsrealestate.com/Find_A_Home/find_a_home.html has plenty of player homes to choose from. All sorted and comes with a description.

If there is one better than Glenvar Castle I don't know of it. It's incredible. Has everything you mentioned and more. Also has 2 very challenging quests for it too. (mannequins not included though. You have to get the mannequin mod too.

http://www.tesnexus.com/downloads/file.php?id=8235

I loved mine so much I revamped the Armory into a full blown display museum.

http://ypdesign.com/tes/glenvar/display.htm

Armoury Lab has most of your requirements,might be worth having a look.

http://www.tesnexus.com/downloads/file.php?id=3791