Practicing with drones is the most effective way to fine-tune your ear. I favor the root-fifth drone for establishing a key center and making yourself aware of the pitch tendency of each note on your instrument. With the drones playing in the background, you will be drawn towards the pure-tuned position for each note.
It is vitally important that you stay cognizant of the center of the pitch, where the tone is most resonant. With the drones in the background, play the note right in the center. If it is sharp or flat, leave it there for a few seconds before correcting. This sensitizes you to the sound of a pitch that is high or low, and makes you aware of when you are pulling the note away from the center. If you are not sure whether your note is high or low, move in one direction and then the other. The drones will make it very obvious whether you are heading in-tune or out-of-tune.
A tuner such as CenterPitch (which will be unaffected by the sound of the drone) confirms or corrects what your ear tells you. Play with eyes closed, using your ear, then check the tuner at the end of the note. Learning the desired display for specific intervals lets you move beyond the equal temperament bias of the tuner. The combination of aural and visual feedback will make a dramatic difference in your ability to hear and play in tune.
Tuning Tactics contains pure-tuned root/fifth drones in each key, as well as over 70 other tracks to develop your ear, as well as text on the art and science of intonation, plus exercises to develop your sense of pitch.
http://www.tuningtactics.com