Spell resistance applies to basically just four things:
- spell/psi-like abilities
- spell/power-completion items
- spell/power-trigger items
(“Powers” being psionic powers, assuming the default magic–psionic transparency.)
Supernatural abilities, command-word items, use-activated items, none of these care about SR. The key here has to be that you are actually casting a spell. Getting the effect or benefit of a spell doesn’t cut it, you actually need the casting process. SR does nothing to non-spell magical effects, even if the rules for those effects are based on some spell.
So if a graft says it allows you to “cast the xyz spell,” then SR applies. But none of them do: the closest they come is “the grafted creature can use poison as the spell,” from the fiendish skin, which is arguable but the absence of the word “cast” signifies to me that this is more like a command-word or use-activated item, and therefore SR does not apply. But the “the ability to continuously see invisibility as the spell,” from fearsome eye definitely does not seem at all spell-like despite utilizing a spell’s description, and the various spell effects of beholder grafts are directly based on the beholder’s eye-rays, which are supernatural and therefore explicitly ignore SR. And that’s literally every graft in Fiend Folio that references a spell.
Since grafts avoid the word “cast,” and spell resistance really is very specific to actually casting spells or doing a very close imitation of doing so (with abilities that use the word “cast”), I don’t think SR applies to anything any grafts do. The fiendish skin’s poison ability is the only one I’d see as debatable, really.
As for updates on grafting, there are more grafts similar to those in Fiend Folio (based on the Graft Flesh feat) in Libris Mortis and Lords of Madness, though neither expands on the base rules, they just repeat them and then offer more grafts (some new, some old). Lords of Madness also has the fleshwarper prestige class, which is all about maximizing grafts.
And for an entirely separate and different take on grafting, Races of the Dragon, Magic of Eberron, and Faiths of Eberron include a new style of grafting, based on separate feats for each type (e.g. Wyrmgrafter for draconic grafts, Eldeen Plantgrafter for plant grafts, etc.). These completely ignore the grafts based on Graft Flesh, and use significantly different rules. (These grafts are still nonmagical, however.) The answer wouldn’t be much different for those than it would for the Graft Flesh grafts, but since you didn’t ask about them I’m going to hold off on actually going through them to see if any use the word “cast.”