Web/software startups worth mentioning in this context (apart from the ones listed up above) are:
http://ffffound.com/ (picture bookmarking service)
http://togetter.com/ (Twitter-based content aggregation and communication tool)
http://garapon.tv/ (TV program recording and viewing service for mobile devices)
http://loilo.tv/ (video editing software)
http://www.jig.jp (mobile browsing and software)
http://www.access-company.com/ (mobile browsing and software)
http://www.vcube.co.jp/en/ (video conferencing service)
Hardware-wise, I would add social camera maker Cerevo to the list:
http://cerevo.com/
These are just some “unique” tech startups coming out of Japan, but there are a lot more, especially in
– robotics
– electric vehicles
– alternative energy (fuel cells, solar etc.)
– mobile tech (cell phones, portable navigation systems etc.)
– video games
– and tons of other areas (3D devices, RFID, OLED, mind-reading devices, medical technology etc.)