I just joined the Fighters Guild and I noticed that all the items inside the FG headquarters are available for me, (previously they where red (stealing) marked as I can recall).
Now my question is, if i loot something and then sell it, will the Guild be mad at me or something like that? Or I can feel free like at home and take every item I want?

Thanks!

They won't be mad at all! They won't even notice.
You are free to take whatever you want, and sell it or keep it for your own needs.

IIRC when you join a guild, all the items belong to you.

Edit: ninja'd

As said above, it is all common property to members of the guild. The mages guildhalls work the same. My character leaves things alone there because if she takes it all, it won't respawn (except for the food) and she would end up with very empty and plain looking guildhalls. That's an important consideration for my girl. Mebbe not for you.

I don't know about the Fighters' Guild, but in the Mages' Guild there are a few areas where items definitely belong to another member. I think in most cases it's stuff that belongs to the Guild Alchemist.

Yeah, you can take as much as you want. For RP purposes though, I only take maybe one sword and one shield. Realistically, the rest of the guild members should get mad if you leave the place barren.

For the Fighters Guild I take only things my character will use and return it to the guild when I'm done with it.
For the Mages Guild I try to resist taking all those soul gems, I usually allow myself 1 soul gem per 2 or so quests completed.

There are a couple of hitches like in Bruma you cant take some of the stuff, so keep an eye on that hand icon. If its red your dead. If its white your alright