Railways
Intercity Rail is a very useful way of getting around the country. They are different in many ways from a rapid transit. They have longer trains, more premium seats, less premium seats, tray tables and all the features of a long train journey ride. I have also included some of my favorites to go and check out!
The Shinkansen, particularly the Tokaido Shinkansen, connects Tokyo with Kyoto and Osaka and travels at a mind-blowing speed of 300 kmph (185 miles per hour) and you reach in just about 3 hours! The other major routes of the Shinkansen include the San-yo Shinkansen (connecting Tokyo and Osaka with Hiroshima and Hakata) and the Tohoku and Hokkaido Shinkansens (connecting Tokyo with Aomori, Hakodate-Hokuto and in the future even Sapporo)
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I recently travelled on the Shinkansen from Osaka to Kyoto and Kyoto to Tokyo. My journey was smooth and very comfortable. I would recommend buying bento or something to eat on the train from the station as no food service is given even in Green Car (the "premium" class on the Shinkansen).
This is the Inter-city Express, or ICE, from Germany. It connects every corner of the country with each other. From larger cities like Munich, Frankfurt or Berlin to smaller towns like Berchtesgaden, Nuremberg and Fuessen. I was going to travel on the ICE on my travels to Germany last year, but due to unforseen circumstances, I had to leave. (Side note - Deustche Bahn, the company that runs all the national and international train services based in Germany, is not super reliable, which is why "zug fallt aus" is an important phrase to learn when going to Germany - there's a high possibility that your train gets cancelled or delayed).
And finally, I couldn't finish without mentioning the Eurostar! It connects London with Brussels, Lille, Paris, Amsterdam and Rotterdam with direct trains and to Cologne, Antwerp, Dusseldorf and more with a connecting service. It runs under the water and travels at 100mph(160kmph) but when it's out of the Channel Tunnel, it travels at 185mph (300kmph).
I recently travelled on the Eurostar multiple times and the experience was outstanding - comfortable, clean seats and while no food service is given in Standard, the Eurostar Cafe onboard has enough snacks, drinks and coffee to keep you going for the entire journey. The separate terminals for international (coming in to and out of the Schengen area) services are, while not air-conditioned, quite well kept and so efficient to travel through, even more than some airports.