I personally am a sucker for roads. Moving fast through my territories is a key factor in my success, as I send reinforcements from behind the lines from my good recruitment centers. This of course is slightly obsolete if you rely on your navy to do your transporting.

I start using sake dens more as I get more territories, being able to leave a province to exploit enemy weakness without having to exempt taxes from previously captured province or worrying about revolts is a great thing. But if you decide to invest some money in sake dens, researching the 1st ninja tech that allows you to build the next level in the building line is couple turns well spent.