Resources
Japanese Learning Resources
I host a repository with Japanese grammar resources, which you can find here. Resources in bold are especially recommended.
What do I use?
Personally, I use Anki and Yomitan with Lapis. Recently, I got a MacBook and I have been using Monokakido's dictionary app more and more. I still use my older Linux (and Windows) setups, but I feel like Monokakido is pretty cool too.