The regeneration is a (Ex) special quality granted by the template, just like the cold subtype. It functions in an anti-magic field.
The Bonecraft armor and every feature it grants, including the Exoskeleton of Undeath, is also an (Ex) ability.
Trollbane won't work. It's an injury poison and Bonecraft armor also makes you immune to poisons (and diseases).
Frostburn damage won't work, since he has the cold subtype and is immune to cold. Vile damage looks like a good candidate for the moment.
Baleful Polymorph would work right up until he finds that armor enhancement that makes you immune to Transmutation spells.
And how do you deal Fire damage to him while he's inside an AMF? With alchemist fire? Unless you rule that multiple applications of being on fire stack with themselves I don't think he'd even care enough to put it out during combat.
And I thought for sure I put it in the first post but clearly I didn't; Bonecraft armor also makes you immune to death attacks. Unless I missed something else obvious, how is Implosion and Feral Death Blow going to get around that? The immunity provided by Bonecraft armor has nothing to do with negative energy. It's just like an undead's immunity, without actually making you undead. The rules compendium defines a death attack in one sentence as any attack or effect which instantly kills a character outright.
MDJ is an option to strip his fire/polymorph protection I suppose, but by RAW I don't think it would do anything beyond that. Five Nations describes Bonecraft armor essentially as a suit of masterwork armor made with a mundane craft check that can only be worn by the bone knight. It even says at one point how the suit can be "further enhanced through magic", in such a way that heavily implies magic is not involved to begin with.
So far Vile damage and vorpal weapons are the two best, if not the most exotic, options. I should have clarified more in the first post but the other problem here is it's not just about killing the character outright. Theoretically this is something that someone would want to play in a campaign and somehow needs to be realistically challenged, not just killed. Doing anything involving the fire protection on his gear involves logical deduction during combat (to find the enchantment) at best, or heavily researching the PC at worst, neither of which is very practical or realistic, IMO.
Or is this simply a concept that should not be played?
But thank you, Bastian, for pointing out that ring... not just because the ring is awesome but also that reminded of the Ritual of the Elements from Savage Species that can grant the fire subtype for 1,440 XP and 36,000 gp.
So that takes care of any lingering doubts from MDJ and anti-magic fields.
What are some of these spells and effects that remove fast healing/regeneration? I know of Graymantle but are there any others, like an environmental or planar effect?