Overall Tokyo is not a digital nomad, coffee-shop working friendly city (or at least not like other major international cities), which was both surprising and disappointing, for me.
EDIT - I'll add the co working spaces I dropped by were all simply terrible. I only went to a few, Open Source Cafe, and Jelly Jelly, and then gave up. I wish I had Tokyocheapo's list at the time. One of them was playing pop music over a speaker system to everyone who was working... I mean, seriously?
I find Tokyo 10x better than SF or LA for places to hang. In SF or LA they are either all full, or you have to by stuff every 2 hours which makes me fat, plus I can't leave anything out so after a coffee or two I need to use the restroom and I lose my space because you can't leave a notebook unattended in the USA. The only exception is maybe the Workspace Cafe in SF.
In Tokyo there's co-working spaces everywhere, they are cheap (especially when you take into account free drinks). Have worked from plenty of starbucks as well, except on weekends when they're full. The one behind roppongi hills that's open till 4am has been great. The one at the corner of Meiji-dori and Omotesando on the 6th floor is huge and been great too. Just don't go on a weekend / holiday.
I'd be curious to know which cities you think are good. I traveled to a bunch of cities in Europe last year and my luck was like yours in Tokyo. I looked up places, checked them out, all were horrible. But I was only in each city for a week or less so maybe I just failed to find anything like you did in Tokyo.
I have a beat up moleskine with some random doodles that I carry around for exactly this reason. Need to use the restroom at a coffee shop? Leave my disposable moleskine and a pencil on the table to claim the spot. If someone jacks the table, easy to ask them what they did with your notebook.
Works in: Bushwick, Denver, Seattle, SF, Austin
You would have to list names of specific places, apart from the ones I listed, because I just don't believe it's a matter of me not looking enough. You would also have to list names of co working spaces too that are good, because as I mentioned, the ones I went to were quite bad.
For SF, I have a map of ~20 hacker friendly coffee shops I frequent there. There were maybe 4-5 coffee shops in all of Tokyo of a comparable standard. (Fukuoka, even Sapporo, had better spots than Tokyo for laptop workers.)
Shanghai is an example of a city that is actually 10x better for working from cafes (if you use a VPN).
I would be thrilled if you would list a good cafe or two, as I am always on the hunt.
+1 Fuglen — gets crowded though, and is quite small.
I spent most of my time at FAB Cafe in Shibuya. They have WiFi, 3D printing, and laser cutters, but I'm looking for somewhere new.
This weekend I discovered Alaska, a cafe in Nakameguro. The coffee was great, although my latte was price-y at 700yen. But food seemed to be around the 1,000 yen mark and it wasn't busy enough for me to feel guilty about hogging a table.
Then how does Starbucks make money then ? Most of the clients in Starbucks in Japan come for a drink with their computer or iPad and stay an hour or even more without consuming anything else - and they have their own internet access via tethering anyway. Yet Starbucks makes huge profits.
With that said for non-chain places with wifi, Streamer Cafe was a short walk from Nakameguro and was a nice place to spend an afternoon. Timeout cafe (Ebisu above liquid room) was reasonable as well, modulo a sales guy using it for an office.
Would be great to sponge a lunch off you someday ;)
The one which I know off the top of my head is Nakameguro Lounge, about one minute from Nakameguro Station. The effective price per hour is 600 to 1,000 yen. Also their lunch menu is really fantastic for only about 1,200 yen.
Also, as it is about two minutes from my apartment, if you're ever passing through Tokyo drop me a line and your coffee/lunch is on me.