I am starting a new character which will be a WitchHunter and would like to get some opinions on what mods would work with this character set-up. My race will be a Dunmer male.

Thanks,
Raed

Assuming that you're basing it on http://www.uesp.net/wiki/Morrowind:Witchhunter#Witchhunter
Not much comes to mid, since most mods dealing with vampires, witches and necromancers are not about hunting them down.

You might want to try http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=8387, which lets you hunt down new creatures, including a witch.
http://www.elricm.com/nuke/html/modules.php?op=modload&name=Downloads&file=index&req=viewdownloaddetails&lid=4121 - a witch hunt

Some new summons, since it is a Major Skill:
http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=6500
http://planetelderscrolls.gamespy.com/View.php?view=Mods.Detail&id=3955

I am using the standard Witchhunter from MW. Thanks for your info.

Raed