The dictionaries that I own have romaji to english and vice versa. I think this is fairly standard. The one that I would recommend is: Its straight foreward and it romanizes よう　as you and not yō.
But I strongly recommend electronic dictionaries like Jisho or Tangorin. (BTW they have a beta version that is awesome
If you have an iOS device I strongly recommend midori. (I think android has a tangorin app)

A note taking program tailored to language learning would be awesome. I know I always get frustrated using Evernote to take notes having to do with language. Maybe it could double as an SRS flashcard system too?

Good luck with your project!