You know what's scary? Things that can't be killed are scary. Here are three suggestions I have to make a scary temple:
1. Remember Facade (the boss from LA and mini-boss from OoS)? Well how about making a dungeon where he IS the dungeon and make him stronger. Maybe at the end of the dungeon, you'll be able to see his true form (like the rest of his body).
2. Have invincible enemies like Traps, Stone Statues, Floor tiles (in FSA statues and tombstones were thrown at you and in tMC and PH pots were thrown at you), Thwip, Thwomp, Mad Thwomp, Hard Beetle, etc... One suggestion is to have a horde of Zombies (the zombies from LA). Sure you can kill the zombies, but they always come back. They are unlimited.
3. I got this next idea from Megaman and from LA: Have a mini-boss that steals the dungeon's treasure (just like Master Stalfos did in LA) but he uses it against you. So for example, if Master Stalfos was the mini-boss you have to make a strategy to kill him, but remember, he has the Hookshot. So with the hookshot, he could zip across the room, and even pull you in so you can attack. Once you've found a good strategy and have killed him, the Hookshot is now yours.

-BGS

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[Credit for my Siggy & Avy goes to my mentor, Lioness]

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