Okay, if I we're making a wizard's tower, or just a generally defensible structure.
If you're the DIY yourself type, Walls of Stone are probably the best bet, but if you don't want to spend a few months casting wall of stone, it may be in your interests to animate a few teams of undead workers and have your apprentices oversee them while you go adventuring.
Walls of Stone are good for basically shaping the tower, but not so much for the volumn. If you want historic 10' thick castle walls, either get your zombies to quarry stones and fill the thin walls you've put up, or just dump a lot of dirt in their, water with a Everflowing Bottle, and get the local druid to cast Transmute Mud to Stone. Make sure to put lead, or medusa's blood, or something in the mortar to block Scrys.
For rooms, you'll want a scrying room, summoning room, crypt, and the usual run of the mill storage and living area.
Being a necromancer, you should contract with the local Church of Evil to cast Unhallow on the area, and if you're the paranoid type, a Dimensional Anchor to block teleports. Some useful spells to have on hand (which you'll need to get through Limited Wish) would be Control Weather, to block armies, and Guards and Wards. G&W is especially nice if you have a maze or similar to really mess with your enemies. Your undead should be immune to the worst effects, so they'll be really effective.
For specific point defense, setting up Wall of Force traps to block doorways, as well as the usual run of the mill symbols and glyphs of warding as well as mechanical traps should be good. Make sure to get guards with Blindsight or Tremorsense to stop assassins, and have some areas only accessable to flying creatures.
And for feats, Craft General should let you build enchantments directly into your tower. A bonus to CL would be pretty useful. Hopes this help.