Yes. All containers that are not degradable, ie. not pseudo-containers (loot/bodies, etc.), are permanent. Be warned, though, that leaving things lying around outside of containers is a certain way to lose them when the cells get reset. You can even store things in Watchers Keep containers in BG2 so that you can 'import' them into Throne of Bhaal.

One of my favourite spots for storing used quest items and sundry things is in the two table containers outside the Copper Coronet; for stuff I need to frequently access in BG1 (central location) inside Friendly Arm Inn and so on. They're safe.

Note that, at least in BG2, there are some areas that are replaced with other areas later on. I believe that one keep that Nalia wants you to save from the trolls will be completely replaced with new areas if it becomes your stronghold.

Also, I believe that you can't re-enter Watcher's Keep once you complete it, so beware.

There's at least one shop in BG2 that gets replaced with another once you complete a certain quest as well. It is worth noting that there is a container in that shop that disappears if you don't buy it before it changes.

(And, of course, there are areas you can't return to, like the starting dungeon.)