I started reading the Mononoke series, then watched the anime. I really loved both and now I'm looking for a manga that has the same feeling, or anything that's on a similar theme to Mononoke, but I want there to be depth in it.

________________
I am the master of my fate;
I am the captin of my soul.
William Ernest Henely

I rate manga with 5 being the average score.

Mushishi, definitely. The anime is also very good, and I recommend you check out both.

Selected Pandemonium in a way.

Natsume Yuujinchou - but it's rather childish, so you might want to give it a try first and see if you like it.

Dokebi Bride , Pet Shop of Horrors and Majo also fit in varying degrees.

Hanashippanashi is great.
xxxHolic has a similar premise - a mostly-episodic story about exorcising Japanese demons and spirits - but it's not as deep.
Maybe you'd like PositioN. It's an episodic series about strange occurences that may or may not be spirits. It's seinen and rather reflective.

thanks ^^ I shall look forward to reading some of these

________________
I am the master of my fate;
I am the captin of my soul.
William Ernest Henely

I rate manga with 5 being the average score.