Lots of stuff about passive defence here, not much about active.
Passive stuff is easy: fail-closed electro-mechanical systems are old hat, and what you can't conveniently lock you can always (conveniently or not) conceal.
But how about active deterrents that won't suffer from decay if they happen to sit idle for a couple centuries? Seems like we should have a lot more examples of those to choose from.
Unfortunately it's going to depend on how many people survived the apocalypse, how long they had and how badly they wanted to protect the base. If the answer to all three is 'enough' then we're in business.
Firstly, let's dig out all those old movies about trapped temples and so on. Get the engineering boys working on ideas for moving floors, pit traps, spike drops, you name it.
Next let's look for ways we can store energy that won't fade over time so that we've got power when we really need it. Chemicals, radioactives and so on aren't going to be reliable for really long time spans, but there's always the overlooked power storage: gravitational potential energy. Put some weights on chains hooked up to the most robust generation methods you've got, seal them in and fill the room with argon or something to make sure they don't get disturbed by rodents 50 years in. Rig it so that some mechanical trigger will remove the support from the weights and boom, you've got power. For a couple minutes anyway. Maybe long enough to get the fire started in your boiler?
Then there's the good old hydraulic method, where you have some hidden sluiceway from the local lake that can be opened to deliver water to a wheel that drives... well, whatever you need it to. Big chunky gears, collars instead of bearings, etc. Doesn't have to be efficient, just robust.
Or how about dropping weights onto piezoelectric crystals? That can generate fairly good electrical sparks. I reckon you could harness that to fire a block of plastique or some other electrically-fired explosive. It would have to be sealed into a chemically inert container to last long enough, but that should be easy enough to do.
There's always power if you look hard enough, and gravity is probably going to be the one that outlasts all the others. In a thousand years the output of your Americium-powered RTG might not be enough to do anything useful, but gravity is still going to be there. Just make sure that your mechanisms are simple and robust and sealed away from contaminants and you'll be fine.
And don't forget to leave a note for the scavengers to find - when they finally make it through your death traps - that apologizes for the fact that you didn't actually leave anything worth finding. Most of it got disassembled for raw materials to make all those traps. Including the one that just sealed off the entrance to this room and the one that's knocking all the supports out from the floor... hey, where did everybody go?
Yeah. I'd make a really nasty GM.