Say a creature has 15 ft. reach and grabs someone at that distance (usually with the Grab ability, but that's irrelevant).
Between the grappler and the grappled there are two empty squares (at 5 and 10 ft.).
While the grapple remains in place, the limbs of the grappler are in the empty spaces.
Now, the question isn't about the limbs actually occupying those squares and acting as obstacles or what (I think that's totally GM fiat, since it depends on many factors... they may be thick arms, thin tendrils, the grappler may be very high so the limbs aren't merely at soil height, etc.).
The question is: what if someone (either the grappled creature or a third one) wants to attack those limbs?
I couldn't find rules about this, as far as I can see, RAW, the grappler is still physically only in the squares he actually occupies, so no one can attack him by targetting one of the empty squares where his limbs are supposed to be.
And yet, it doesn't make sense. Rather, it's really common sense that if one friend of yours (or yourself) get grabbed by long tentacles, the first thing you try is cutting them off.
So, how would (or how DO) you handle it mechanically? Let the creatures attack the limbs in empty spaces? And what happens? How do they get cut off? How does the grappler release the grapple?
You're putting in more stuff than what the rules actually say.
The rules for the PC being grabbed by the creature is that the PC is pulled adjacent to the creature, and that if no space adjacent to the creature is open, the grapple automatically fails, and nothing happens. That's it.
The whole "limbs moving through squares" thing is not defined anywhere in the rules, which means any mention of that being the case whatsoever is wrong, and not founded anywhere except at your table. At best, you can argue that a creature can only affect certain squares with certain weapons, in which case you'd be correct, as one example is a creature having a 10 foot reach natural attack and a 5 foot reach natural attack. But, that's irrelevant to typical reach, which is what the question is all about.
Of course, regardless of what the reach actually is, you don't need to worry about limbs or anything like that any more than you would other subjects. If I'm trying to attack an enemy through a 5 foot wall with Reach, it won't work because I have no line of effect to that enemy, even if the range itself isn't an issue, or even if I can actually see into that square. The fact that I can't affect a square because my means to execute the attack is thwarted by a wall granting complete and total cover, makes having that 15 foot reach with whatever natural attacks I have, irrelevant. Similarly, just because I could theoretically reach my limbs into that square, doesn't mean that the PC behind the wall can properly affect me back, because the wall in question is likewise blocking his ability to affect (or see) me.
In other words, you can't attack limbs directly unless you have specifics stating otherwise, such as sundering a Hydra's head. There's the Called Shot rules, but they're optional, and still requires targeting a specific creature, and really only applies penalties or restrictions to what the creature can do. It says nothing about actually targeting the limbs of that creature.
**EDIT**
There's also the Strike Back feat, which best represents what you're looking for, but that lets you ignore the factor that a creature can reach into your square, and you can't reach back into its own square. It still has nothing to do with limbs.