I have had it a number of times. Twice last December, once at a small place in Tsukuba and once at Kozue (the Japanese restaurant on the 40th floor of the Park Hyatt in Tokyo). In Tsukuba it was just fried fugu and it was quite good. At Kozue it was a complete dinner, each course was fugu. It is a special dinner they do there. I have had it a couple times (3 or 4) at Kozue and a couple times at Edo Gin. I enjoyed all of them. In addition to the toxin I think the fish has a very nice, subtle flavor and interesting texture. It isnt just the liver that has the toxin, I believe the blood and I know the ovaries have the toxin. In fact the ovaries have extremely high toxin levels. I think one reason that they do it mainly in winter is that the toxin levels are lower because the water temperature keeps them from spawning. I think toxin levels go up in the spring when they start to spawn.
I think I read somewhere that in addition to having non-poisonous varieties, the chef, by nicking arteries more or less when preparing the fish can serve varying amounts of the toxin with the fish. Im not sure if this is true or if it is common practice. I would say however, that if I had to guess, I would say there is less toxin in what I have had at Kozue than at Edo Gin. Perhaps it is my imagination, but I thought I could really feel it in my mouth and on my tongue at Edo Gin. One thing I noticed in particular was that even though the sashimi was ice cold (when felt with the hand) it felt warm in the mouth. One of our Japanese friends at the dinner said that was typical in some people, others felt a tingling sensation.
As far as where to go I cant help in Kyoto. In Tokyo I would recommend Kozue. The dinner was excellent and the view fantastic. Edo Gin was in the basement of an office building although the food was good. However, Edo Gin also served a custard of fugu semen with the all fugu dinner that would have been a bit over the top for us westerners; that is if our Japanese friend had told us what it was before rather than after we ate it. A very knowledgeable restauranteur in New York, who is from Tokyo told me he would recommend Kyubei in the Ginza area for fugu in Tokyo.
Also be aware that it is quite expensive, especially for the all fugu dinners. They are in the range of $150-$200 per person, not including drinks at Kozue or Edo Gin. At Kyubei I dont know but given general prices at Kyubei I would expect it to be more than that. Also, at least at Edo Gin we had to order a day in advance. Note that there is more than one location for Edo Gin and not all serve fugu. Some Edo Gin locations dont take reservations either but we were told that we had make reservations and order the fugu in advance. This limited us to some of their locations. Im not sure if that is true at the others but it would be worth checking.