An item is allowed to have additional magics added to it, where the cost of the addition is the cost of the final product minus its current value. That is, take a +1 quarterstaff (2300 gp) and make it a +2 quarterstaff (8300 gp) for 6000 gp. See Creating Magic Items – Adding New Abilities:
Adding New Abilities
A creator can add new magical abilities to a magic item with no restrictions. The cost to do this is the same as if the item was not magical. Thus, a +1 longsword can be made into a +2 vorpal longsword, with the cost to create it being equal to that of a +2 vorpal sword minus the cost of a +1 sword.
If the item is one that occupies a specific place on a character’s body the cost of adding any additional ability to that item increases by 50%. For example, if a character adds the power to confer invisibility to her ring of protection +2, the cost of adding this ability is the same as for creating a ring of invisibility multiplied by 1.5.
For many items, combining functions (rather than upgrading them as with weapons) in one item carries a price premium equal in value to half the value of any functions after the first. This would also be part of the cost of adding magic to an already-magic item.
Stuff like directly using hides or medusa heads to make items, kind of. By default, yes, your character needs to have the appropriate materials (whose worth equals the crafting cost of the item), but what the “appropriate materials” are is left undefined and up to the DM.
Thus a DM may decide that a spike, gem, etc. is worth a certain amount towards the crafting cost of the item (e.g. that sword costs 2000 gp to make, but the gem you just found can be used for a part of it: you only need to provide materials [steel, leather, whatever] worth 1000 for the remainder of the sword). Most of the time, though, it’s more like “I go to the blacksmith and buy whatever I need for the sword from him.” Requiring specific, especially rare, materials doesn’t really occur in the rules except sometimes for certain spells (e.g. raise dead requires diamond dust).
I haven’t personally seen one, but I’d be surprised if no one’s drawn up lists of explicit materials for particular items. I doubt it’s official, though.
The Detect Magic spell states:
If the aura emanates from a magic item, you can attempt to identify its properties (see Spellcraft).
Spellcraft states:
Identify the properties of a magic item using detect magic: DC 15 + Item's CL
So what, you might ask, is a "property?" Well, they don't define in a legalese way exactly what is included in a magic item's properties, except to note that it definitely gets you command words ("The spells detect magic, identify, and analyze dweomer all reveal command words if the properties of the item are successfully identified..."). One simply has to assume from general English definition and logic that it gives you anything beyond that, including what the item even does.
I think it's best to interpret "properties" as "All of what it does, including charges, command words, and whatnot. Its full rules stat block." (Excepting, of course, other defined exceptions like artifacts and spells on a scroll.) Analyze dweomer specifically says it gets charges, but relying on a 6th level spell to get the charge level of a plain old wand is pretty lame IMO.
In earlier editions of D&D I was fine with not telling people charges and letting them find out when they ran out - it added a nice randomization factor - but in Pathfinder where the Christmas tree syndrome tends to dictate that it's players' God Given Right to liquidate all treasure for a union-decreed cost to buy other gear, not knowing charges and thus value would be an impediment.
Best Answer
Clockwork prosthetics should be affected by magic suppression the same way constructs are, and necrograft arms and legs should be affected by magic suppression the same way undead are. Which is to say,
(emphasis mine)
So the graft itself is not affected; a clockwork or necrograft arm continues to function as an arm, at the very least.
As for their special abilities, if those are magical they would be suppressed by antimagic field or dispel magic the same way the spell-like or supernatural abilities of constructs or undead would be. However, most of them seem very much physical functions of the graft. Clockwork arms and legs allow you to lift more, because they are stronger. Undead flesh is often tougher and doesn’t tire, hence the advantages of the arms, legs, and sallowflesh. The strangler’s tongue comes from a mohrg, whose paralysis ability is probably Extraordinary (though it does not actually say, supernatural paralysis is usually explicitly marked as Su; see the lich’s paralyzing touch for example). Even the enhancement bonuses provided by several of the necrografts seem to me to be non-magical in nature: nothing about enhancement bonuses says they must be magical (though they usually are), and the explanation for why they impart these bonuses are all very physical.
Really, the only two I find questionable here are the ghoulgut and gravegland necrografts. These provide more active effects, which could conceivably be separate magic effects suppressed by antimagic field or dispel magic. The ghoulgut still seems pretty physical to me, but I can buy it being magical. The gravegland is even more apparently magical; I could accept an undead organ having non-magical access to negative energy, but it is a stretch. I’d probably allow it if I were GM, but wouldn’t expect others to.
Finally, I would point out that these grafts’ antecedents in 3.5 were more detailed. Grafts appeared first in Fiend Folio, and were also found in Libris Mortis, Lords of Madness, Races of the Dragon, Faiths of Eberron, and Magic of Eberron. These have many more rules, as well as many more grafts, which may be useful to port to these Pathfinder options. In fact, these books actually present two different types of graft: the “old” style in Fiend Folio, Libris Mortis, and Lords of Madness, and the “new” style in Races of the Dragon and Eberron. These differ in a variety of ways, so I leave investigating how or whether you want to use one or both in Pathfinder as an exercise to the reader, but of relevance to this question, both styles explicitly state that the graft, once applied, functions in its entirety even without magic.