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Obviously the first series that comes to mind when comparing to Hell§ing. Instead of vampires hunting lesser vampirse, witches are hunting other witches. In Witch Hunter Robin, an elite group of witches, (some are called "craft users,") hunt down other witches when the government discovers that their powers have manifested. Imagine a world-wide bureau that keeps a genetic record of every person who will eventually develop "supernatural" powers.. and when the person, come puberty or so, manages to unlock his/her powers, that government bureau kills him/her. That is the beginning of Witch Hunter Robin... an interesting series with a few twists, to say the least.
Okay... 1. Both main characters possess surreal power beyond those of their peers.. .. but these powers either lay dormant or mostly used neutrally until later in the series. 2. Both involve magical entities beyond the control of "normal" humans. 3. Some of these magical forces are not main characters - they simply *exist* in the world. 4. Both stories have a significant portion of them dedicated to background information near the beginning - the Violinist of Hamelin moreso than Scrapped Princess. 5. Both are "quest" animes with a theme of magic - although the "magic" in Scrapped Princess is more like human/alien warfare the magic in the Violinist of Hamelin is definitely "magic" magic.
I hate to make a trite comparison.... but the "quest" format of the Violinist of Hamelin is not quite like Berserk's... but the concept of Demonic humans who save the world from some overbearing evil is definitely similar. There isn't as much blood... and there is definitely more *active* magic - but the two have a very interesting feeling for them that I just can't shake.