Two suggestions I just thought of overnight: they're rather esoteric though, so maybe not what you're looking for.
(1) The Far Realm Has Different Physics
Okay, yes, that's obvious at a glance, but take a step back for a moment and consider what that really means in a game context: the rules of the game are, after all, supposed to represent in some abstract, dice-rollable form what's really taking place in the world of the PCs, right? The Far Realm is supposed to represent something beyond the gods' creation entirely, something so alien and corrosive to existence that its advent means the end of everything the PCs know.
So maybe Far Realm creatures play by different rules.
The best way to demonstrate what I mean is with examples, I think. Say you want to make use of some of the excellent Far Realm beasts presented in old 3.5 books like that edition's Fiend Folio. You put your PCs up against a Skybleeder (CR 12, so hopefully much later in the game here!), which has Regeneration. Now, the rules for Regeneration changed from 3.5 to Pathfinder: in 3.5, the way it worked was that a critter took nonlethal damage from everything except the damage types that got past the Regen; in PF, Regeneration is just Fast Healing with the extra proviso that it keeps working after "death" and that taking damage of the "bypass type(s)" actually shuts it off for 1 round. Now, normally, when you bring a critter from an old edition to the present one, the present edition's rules take precedence; in the Skybleeder's case, you're supposed to treat its Regen as Pathfinder Regeneration.
My proposal here is that you don't do that. The Skybleeder, being from the Far Realm,
literally plays by different rules than the PCs.
Likewise, say you have a Pseudonatural Werewolf to send after them; Werewolves, of course, have DR against Silver. Now, one of the changes that PF made to DR is that a weapon with a high enough "plus" can bypass DR that's based on material or alignment (the table is on page 562 of the Core Rulebook). So if the party Fighter has a +3 Battleaxe, he can get past a normal Werewolf's DR, even though the DR is of the /silver type. But with a
Pseudonatural Werewolf, the critter is playing by the old rules, which say that the Fighter is just plain SOL unless his axe is made of silver (or if he's using Silversheen, or one of the spells that changes a weapon's material for the purposes of overcoming DR, etc.).
You may or may not be able to make use of this suggestion, depending on your level of system mastery; your OP said you're relatively new to the GM's chair but that does not in and of itself mean you're new to the game. If you're an old hand at earlier editions, then this should be possible (perhaps even easy) for you to pull off. Doing it successfully pretty much requires that you never tell the players you're doing it, of course; it should be a subtle change; many if not most times it won't even come up in play. But when it does, knowledgeable players will wonder what the Hells is going on- the creatures will seem that much more "wrong." They might accuse you of forgetting the present rules, if they notice that you're using the old ones; if they do, you can choose to either say "Oops, you're right! Thanks" and use the PF rule, or invoke Rule Zero (the GM is always right) and say "Nope, I'm doing it right. Strange how that's working, isn't it?" There will be even more differences if you pull a 3.0 edition monster into your PF game, of course.
This sort of stealth rules-change won't make a huge difference, granted, and it may be too much effort for not enough reward- but it's another way to make Far Realm critters seem off-kilter and to emphasize that they really are Alien to the PCs' reality.
(2) Madness Does Not Equal Evil
A lot of people who use the Far Realm forget this, and treat the Far Realm as basically just another level of the Abyss, only with more tentacles and slime. That's self-limiting, though, and doesn't really do the concept justice; the real nature of the Far Realm is supposed to be a place that's so far beyond any plane of existence the PCs know that the very
conceptual underpinnings of reality are different. One example is that the description in the 3.0 Manual of the Planes notes that creatures exist there on more than one layer simultaneously; in any sane plane of reality, that's impossible by the very definition of a planar layer. Insanity, though, just means "irrational, alien, disordered thought," not "selfish, wicked, uncaring of others" (the definition of Evil alignment). There's overlap between Evil and Insanity of course- just look at Jason Voorhees from the Friday the 13th movies- but there's also overlap between Insanity and Good.
This has actually been used a few times in D&D; one case was in a 3.5 monster book from a third-party publisher called The Inner Circle, who put out a campaign setting called Avadnu under the imprint "Violet Dawn." They made a PDF called "Legends of Avadnu" which was a supplement to their world's bestiary, containing a race of monsters called Lumina; part of the description for Lumina as a race states that
Legends of Avadnu said:
Lumina originate on a plane of infinite wonders, a place where goodness and beauty are integral to existence. However, their home is also so unlike most realities that it can be maddening; fire, light, and thought itself are among the elements of their world that differ wildly from those found elsewhere. In many ways, lumina are closer kin to beings such as pseudonaturals and neh-thalggu than they are to celestials.
Three types of Lumina are presented in that book; all are Epic-level foes so probably not anything you'd actually want to use in your game. But the
point of the Luminas' existence is still valid: the Far Realm can contain heroes or altruists too.
What this means, to your game, is that there may be a way for the PCs to "win" (by which I mean, stop the invasion of the Old Ones) if they can somehow make contact with creatures from the Far Realm that are not intrinsically Evil in addition to being just Insane. The Good Far Realmers like Lumina may find your reality so intrinsically warped and horrid that it corrodes their very thoughts, and therefore hate it and wish it "purified" or eradicated, but... maybe they can be communicated with and persuaded to accept the notion that just shutting it away again is good enough. Maybe they are sickened by the portions of your multiverse that the "eaters" are bringing through to the Far Realm and devouring, and they'd just as soon see the
Gates the eaters are using to do that permanently closed; since they're from the Far Realm themselves, they probably have powers on a similar ridiculous level as the Entities that are invading the PCs' own existence. So maybe by acting in concert with the PCs somehow, they can shut down the portals and prevent the apocalypse.
Of course, even learning of the existence of such Entities is likely to be fraught with peril and numerous opportunities for permanent loss of sanity on the part of the PCs in its own right. And you'll need to answer the question of why the gods haven't tried to contact the Good Far Realmers themselves, of course; but that one can actually be pretty easy: desperate people, you see, usually don't think very well and end up doing stupid things. The gods are clearly desperate, as demonstrated by their shutting off the Divine Magic spigot and letting the fiends step in to take over. So they're probably not even thinking of alternate possibilities like the existence of potential help on The Other Side. Alternately, maybe the Good Far Realmers are terrified by the power of the gods, and see them as a prime reason to allow the destruction of the existence they hail from; tiny and near-helpless creatures like the PCs, though, are more like toys (cue Aklo translation of "Oh look, they're so CUTE!") and thus, more likely to capture and hold positive attention.
This, of course, is most useful if you actually want the PCs to be able to "win-" if you're really dead-set on having Reality Go Boom, then hey, more power to ya (or rather, more power to Azathoth/Nyarlathotep/Shub-Niggurath Cthulhu Rllyeh wagh-nagl FTHAGN!).
