One thing is for certain: most Japanese coffee is baaaad. It's watery, flavorless, and utterly unimpressive. Thankfully, other options abound.
1. Doutor Coffee is a chain cafe that sucks even worse than Cafe Beethoven. Avoid at all costs.
2. Excelsior Caffe is a chain that has pretty good coffee. Not great, but not hard to find, and not too expensive.
3. There is a fucking Krispy Kreme in Shibuya. The coffee is fine, and they have neon-green doughnuts shaped like cats.
4. There are a number of Tully's Coffee outlets here too. Tullys is okay in my book.
5. Ah, Starbucks. The gold standard of chain cafes, where you will pay about $3.75 for a grande cup of drip coffee. Ow. But then you remember the humiliation you experienced at the hands of the staff at Cafe Beethoven, and you know it's worth every yen. By the way, don't expect free refills on drip coffee. But make sure to retain your Starbucks receipt. You'll see the words "one more coffee" printed there. Take that receipt to any Starbucks (on that same day only) and get another cup of drip coffee for a mere ¥100 ( about $1).
6. In some conbinis, on or near the front counter you'll see machines that make one cup of coffee at time. Basically, you'll have four choices: hot latte, iced latte, iced coffee, and hot coffee. These one-shot machines are usually about ¥150, and they make decent coffee. Pay for it first, then a clerk will give you a cup. Brew. Drink. Awaken the coffee beast within.
Questions? Feel free to contact me directly: firstname.lastname@example.org