You can keep them anywhere really, just not in the trash cans. Or on the ground. Sometimes if I'm feeling humorous I keep my stuff in the dried herbs on the Black Root herbalist's walls.
I prefer locked barrels. I don't trust those people running around, you know. The rat warehouse makes a good storage place indeed. Also, after you complete the first quest for Madam Lil, you have an empty house with a chest, which you can use for keeping your stuff there.
What are good houses to live in Arcanum ?? Not inn( cost money ), and not houses where i cannot sleep ??
Simon's warehouse in Tarant has lots of storage bins close together. You can easily categorize yur wares - books in one place, offerings in another, tech ingedients in another, etc. Late in the game when it's no fun encountering weak monsters in the wild, run arcanum with the -norandom switch to get rid of them; then going to and from your warehouse is pretty quick.