Pretty much the only unsafe places to leave something are Malcolm's house (before buying it, and especially before turning him in) and the room in the Ducal inn (though you can re-rent the room to get your stuff back if your time runs out).
It is convenient to leave your stuff near a house with a bed, but it is just as easy to make a hay bed beside a teleporter and leave your stuff there. You can take over any building, but if you pick one that is occupied, you will have NPCs wandering around getting in your way. Get the portable bed from the house north of the cursed Abbey (lots of room, handy teleporter pad) and you can setup wherever you want.
