Some thoughts-
Protection from Divination
A.- Mordekainen's Private Sanctum protects against all scrying from outside, can be made permanent, has a decent area. Not a bad choice, for a 5th level spell.
B.- Screen Allows you to fool incoming scry attempts with no save, and replace whatever you like. Harder to get over a long time, but has a 24 hour duration, if memory serves.
C.- Hide the Path Prevents Find the Path from working at all, and forces a CL check on all divinations of 6th or lower. Not perfect, but works well. MASSIVE area, too.
D.- Don't underestimate lead lining. A stronghold space can be lined with lead pretty cheap, all things considered, and is a no-save protection for a lot of spells- and it's immune to Dispel Magic, too. Good to use in combination with the other spells.
Immunity to Planar Invasion
The bread and butter of this is Forbiddance. Huge area, permanent duration, no save protection against incoming planeshifters. The extra effects are nice, but not the key draw of the spell- it has a flaw, though, in that it blocks all incoming shifts, good or bad. Okay on the Prime, but not so good for Genesis, etc. Which is where Zone of Respite comes in handy. Also blocks incoming, low level spell, but does NOT block already existing portals, allowing you to build a front door, secure it and forget about unwanted teleporters. You'll need to build it into a custom item, though- shouldn't be too expensive either way.
Immunity to Tunneling
Impossible as far as I know. Somewhere, something has the patience to dismantle your walls, and making them out of force and obidurium will bankrupt you or your suspension of disbelief so fast your head will spin. BUT- how about layering massive volumes of packed earth with iron walls? A tenth as cheap, and almost as good. Prevents Disintegrate unless the caster has more time than sense, and Passwall and its ilk can't get through anything as hard as iron.
Locked Doors
LOTS of options here, so I'm just going to give you some spells.
In no particular order:
Improved Arcane Lock
Arcane Seal (Magic of Eberron)
Sign of Sealing (+Greater)
Portal Alarm (+Greater)
Alarm, Greater
Mundane ways to forbid entry-
Really big doors. Knock only affects a small(er) area, and you can build a much bigger door for relatively cheap rates Plus, makes the strength DC much higher to force them open. AND it's much more interesting to have a 30-by-60 foot door, anyway, don't you think?
Locks. And antimagic. Amazing locks are very cheap for the price, and can take a while if you have multiple locks on one door, and the intruders can't use their favorite intrusion spells.
In summary these options can give you a pretty damn secure tower- not immune, and not impervious, but remember the key point of physical security- anyone can get in with enough time, and these options are the best I know of with years of keeping an eye out. If someone wastes ten disintegrate spells just getting through the barrier of earth, they've wasted thousands of GP, relative to the 250 it took to put up the earth wall for you. Or they have to do it very slowly, which gives the players time to wake up and knock back.
Hope this helps!