That's quite a list!
In Tokyo a day could look like the following.
Wake up early for the Tsukiji Fish market, after head to Shibuya to see the city wake-up and see the local culture. After head to Harajuku, it's almost around the corner and the Meji Shrine can be visited here as well. Enjoy a lunch over at Omotesando and head to Ryogoku Kokugikan for the noon, Asakusa is very close here and you could visit Sensoji as well (this is a big recommendations). Then at the end of the afternoon, head to Tokyo tower or the Skytree (the last is close to Asakusa) and enjoy the Skyline view of Tokyo. Enjoy a dinner of your choice and head to Ebisu for evening fun.
En next day you could visit some places which take up a little more time. Start with a morning walk in the gardens of the imperial palace, then head to Akihabara to try out some of the arcades and see electronic city for yourself. You could then spend the afternoon around the Gibli museum and spend the evening in a place of your own choice - or head to Ebisu there was not enough time on the previous day.
Day 3 could be anything from a day trip to Fuji, to more exploring in Tokyo. For instance go Sumo watching if there's a match on. More about Sumo HERE.
Kyoto and Osaka are much easier to travel around in, basically because they are much more compact. The key here is to look at the map and combine places that are close together. For instance in Kyoto, it would not be hard t combine International Manga Museum, Shijo Dori (visit Nishiki Market here as well), Kyo Ryori together and add a visit to Kiyomizudera as well. Arashiyama and the Golden pavilion are to the west and could thus be easily visited together, while the Silver Pavillion and many other worthwhile temples are to the east. Oh and Toei Studio park is in the middle of nowhere :D
In Osaka Namba Yasaka Shrine, Dotonburi and National Bunraku Theatre are closely together. The other places are all over the city and could be visited in any order.
Let me know what you think :)
Daniel