The Collage gives you a free room but do either the thieves or dark brotherhood give you the same? A safe place to store loot?

Yes

I don't know about the Thieves Guild, I haven't played it yet.

the thieves guild i believe does not give one

The Thieve's guild gives you a bed to sleep in but that's as far as I have got in the storyline. I'm sure there will be a house type reward at the end though.

correct me if i'm wrong but:

define "house"

you can have a safe bed/place in both the ragged flagon and in the DB sanctuary. finish DB and you get your own bedroom

I can confirm that the chest by your bed in the thieves guild hall does not reset and you won't lose your stuff. I stored some armor in there for awhile. You can also use the bed. You can also use the Nightingale Sanctuary; it has beds, chests, lights, etc.

For the Dark Brotherhood you can use one or both sanctuaries if you want, pretty sure nothing resets there as well. Just make sure you keep a save.

If you complete the Thieves Guild quest line, you get an upgraded bed in the cistern. Not much though, little privacy wall, a chest, and nicer set of sheets.

I was kinda hoping the Thieves guild would reward you with

Also in the Thieves guild you should take ownership of Goldenglow Estate, and Honningbrew Meadery. Then muscle Maven Black-Briar out of business, and see her homeless and destitute, begging on the streets of Riften.