Thought I would share my cargo issues with ya.
Hardtop on:
I mounted these:
http://yakima.com/Product.aspx?id=163
They are a two part, one is a pad that permenantly mounts to the roof, the other part is what that link is. This means all you have to do is spend $30 on the "pads" for each vehicle you want to remount the system on to.
You have to drill 8 small holes only and the "landing pad" seals with silicone. Then all you need is crossbars (like $50) and it distributes the weight perfectly. I have a large cartop carrier (enclosed yakima box) that I STUFF with tree climbing gear on a daily basis and there is no flex in the hardtop at all. (about 125 lbs with chainsaws)
And with the crossbars on, its stout enough that I can lift the hartop off the jeep using only the crossbars.
Hardtop off:
Yakima makes a basket called "basket case"
http://yakima.com/Product.aspx?id=71
This is the PERFECT size for in between the rear rollbars & even fits with a soundbar installed. I have mine mounted with heavy duty zip ties. It sits low enough so you can put your hardtop on over it, but it is high enough up where my 2 labs have enough head room to stand up completely (this all based on having no back seat)
That basket can take a pounding. It is about useless with the top on though. But man, it works GREAT. I load it with about 90lbs of gear all summer with no flex.
It looks pretty freakin cool too!
I found these that are new this year from olympic:
http://www.quadratec.com/products/12037_500_07.htm
I am STOKED about this, I almost had this same type of set up custom fabricated last year so I could keep my cargo box on with the top off, it adds a buttload of lockable storage.
Sorry I went on about this, I consider myself a pro at Tj storage though!! (I have been a victim one too many times!!)
Hope it all helps!