What are some scenic sites or nature spots in Japan that you had long heard about and which didn't disappoint you when you saw them for the first time?

Fuji-san. Golden ratio in nature.

鋸山 (のこぎりやま Nokogiriyama) in Chiba prefecture: https://tokyocheapo.com/entertainment/view-nokogiriyama-hiking-chiba/

I second Fuji-san. Photographs can't do justice when you see it in person, especially during sunrise and sunset

Itsukushima Shrine, torii gate.

Yakushima... it's a magical place

Kamikochi in the red leaf autumn. Japan Alps in the snow winter. Shinmaiko Beach Tatsuno in the Spring. Matsumoto Castle in the spring/autumn or full moon. Suwa Lake and the fireflies.

The view from the top of the mountain in Hakodate. Magnificent! Would be perfect if they didn't have horrible canned music blaring out from the speakers!

Shakotan coast in Hokkaido.

The 200+ cue line going up Mt Fuji never disappoints.

Gonna second Nokogiriyama and Yakushima.

No votes for Kabukicho? Weird.

Night skyscrapers which you can see when you drive on the Metropolitan Expressway. That's really wonderful and magnificent. That always makes me think that I would live there if I had enough money.

What are some scenic sites or nature spots in Japan that you had long heard about and which didn't disappoint you when you saw them for the first time?

The many gorges I’ve been to in the south, but mostly the ones I’ve never heard about or made a special trip for, just stumble across them on a camping trip, drive, etc. Especially taking a wrong turn and finding those beautiful green valleys filled with rice fields.

None. But there have been plenty I did NOT know (much) about beforehand and that wowed me. Yeah, Yakushima and the torii gate at Itsukushima, are quite the thing, but what I think I've loved most are the little things: hiking in the mountains Kagoshima and realizing that I head no sound at all, and that it could have been anywhere. Driving along very scary and narrow cliff rows (with no guardrails) in Shikoku on the way to Kochi and seeing a beautiful lake below. Or the beauty of Tateyama covered in snow on your left, and the ocean on your right, with but a couple of kilometers in between, in Uozu, Toyama.

Mt. Fuji? Overrated.

Kamikochi. Absolutely beautiful, especially on a crisp late fall morning.