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I am playing a gestalt game as a Wizard/Alchemist. The Wizard gains a familiar via Arcane Bond, and the Alchemist gains a familiar through the Tumor Familiar discovery.
Does the fact that the familiars are coming from two different classes with differently named abilities legitimately grant me two familiars?
No, you do not get 2 different familiars. Familiar levels stack.
From the Familiars entry:
Levels of different classes that are entitled to familiars stack for the purpose of determining any familiar abilities that depend on the master's level.
You can though have a familiar and an animal companion (but remember PFS rules only allow for one combat companion at a time). From same source:
Only a normal, unmodified animal may become a familiar. An animal companion cannot also function as a familiar.
If you count third party sources and take a feat (extra familiar) specially for that purpose, you can have a second familiar, but as said in the answer by briddums, you don't get an extra familiar for different classes that grant it as a class feature.
Multiple familiars are possible in Pathfinder, but only if they are gained from the same class. The simplest way to gain multiple familiars is as a Cleric.
Clerics gain 2 Domains at 1st level. The Crocodile domain grants a Dwarf Caiman as a Familiar as one of its domain abilities, likewise the Monkey Domain grants a Monkey familiar as one of its domain abilities. Thus a Cleric with these two domains would start with both a dwarf caiman familiar and a monkey familiar, which would both advance according to your cleric level + levels in any other class that grants a familiar.
You can also get familiars from the Vermin Domain, Eagle Domain, Frog Domain, Plane of Air/Earth/Fire/Water Domains, and Serpent Domain -- all of which are species specific.
If you want to really stack familiars, the 3rd-party Magus archetype the "Tovenaar" grants 2 Domains at 1st level, another at 2nd, and more as you advance in levels, which could grant you all of the above, plus an additional familiar if you take the Familiar magus arcana.
