I think you got some excellent ideas already! Here's my .02
The first storage pic you posted (not the bunkbeds one) - the one with all the plastic bins - while it is a decent amount of storage, is STUPID. I shy away from those because of the "DUMP" factor That many removable bins full of small objects are just begging to be dumped. I have seen this downfall at several friends' houses, and that's why we have not fallen into that trap
I prefer a regular deep bookshelf with baskets/bins/whatever if necessary. Obviously big toys sit by themselves, we have a "vehicles" basket, "guys" basket - like little bendy guys, action figures, etc., "instrument" basket (obviously not all instruments can go in, but little maracas, and glockenspiel and harmonicas and stuff can). We have a lego basket that got dumped too much, so I found a nice picnic basket that had a wooden lid on it, and slid the basket under an end table in the living room. It's not dumped nearly as frequently now! I guess that's all our baskets I can think of ... well, no there's one in the kitchen with cutting foods for my 2yo.
Did that help at all? I don't go for spending lots of dough on stuff like that. DH made our bookshelf in 1/2 a day. Coulda bought one from the local classified paper, but I'm too lazy to drive around town looking at them! All our baskets are NOT matching and are from the thrift. I especially like to grab produce baskets when I find them ... the one with metal handles with a wooden grabber on top ... those double nicely as berry picking/pine cone gathering/collecting baskets. And baskets at thrift stores & yardsales cost about 50 cents each, so I dont' really care if it gets stepped on one too many times and crushes