Q:

How can we take the ontologies of our best physical theories seriously?

It seems to me that numerous features of our best physical theories thus far (most notably in my humble and near-meaningless opinion: the whole notion of renormalization in quantum field theory) themselves strongly hint at not taking the ontology of such theories very seriously. 
To give a standard example: the BCS theory of superconductivity shows how one might come up with a theory involving only Cooper pairs being behind everything, where the electrons forming these pairs interact at a point, but this can also be understood as an effective theory in which the interactions are actually mediated through phonons. The ontology of the first theory seems to consist merely of the electrons forming the Cooper pairs, whereas the latter has the electrons as well as the phonons. The point being: without the ability to experimentally probe regimes smaller than the length scale characterizing the Cooper pairs, one could not distinguish between the two theories, though they have different basic constituents.
Given the further fact that we do not, and likely will never, have infinitely precise measurement capabilities, we can never be sure that the zoo of basic building blocks used in the descriptions provided by the best theory available for a given physical phenomena are actually.... well, there. How can we ever take the "particles" or "fields" (etc) appearing in physical theories seriously as being actual entities in the physical world? Despite having just asked a question... what I really want to ask is:

Question: Does anyone have any suggestions for good references addressing this issue? Something making clear, insightful arguments for or against such a perspective (or, preferably, both)? Also, references that specifically address how this can be thought of in terms of quantum field theory would be nice. :)

A:

For a rather technical book in philosophy of quantum mechanics and QFT you can read Laura Ruetsche "interpreting quantum theories". 
You will also find numerous articles there (I link to subject pages, but you can browse the whole site):
http://philsci-archive.pitt.edu/view/subjects/quantum-field-theory.html
http://philsci-archive.pitt.edu/view/subjects/fields-and-particles.html
As you seem interested in the question of scientific realism, you can also read on this general issue (for theories in general, not QFT in particular), and the related issues, such as underdetermination (the problem of having two empirically indistinguishable theories) or constructive empiricism (the most influencial contemporary anti-realism). You can check all these subjects, including QFT, by doing a search on the stanford encyclopaedia. That's a good starting point to find references on a subject.
http://plato.stanford.edu/

A:

On philosophy of renormalization specifically the canonical reference is Cao-Schweber's Conceptual Foundations and the Philosophical Aspects of Renormalization Theory, see also Butterfield's Reduction, Emergence and Renormalization for a more recent take. There is more or less a consensus that the ontologies of quantum field theory are of a transient as-if character. After all, the essence of renormalization is to cut off the contributions from the inaccessible high energy objects, and produce an effective theory, or rather hierarchy of theories, which are necessarily non-fundamental. But there are two opposing views as to the import of this hierarchy of effective field theories (EFT). To some, they are a prelude to a fundamental "theory of everything" (be it string theory or something else). As Cao-Schweber describe:

"In the last three decades, neo-Platonists working on fundamental physics, within the context of QFT, have taken ahistorical mathematical entities and relations, particularly gauge symmetries and supersymmetries, and their representations, as expressing true reality and/or manifesting the hidden essence existing beneath overt phenomena, both in terms of entities and their structural patterns. By revealing themselves in the real nature of various phenomena, they are appropriated to constitute the universal foundation of physical theories."

However, the EFT hierarchy poses particular challenges for such traditional physical Platonism. Specifically, the so-called decoupling theorem suggests that even if we postulate some "fundamental ontology" at the top of the ladder it will not manifest at all at the rungs accessible to us, and the theory of these intermediate rungs is structurally unrecognizable compared to the "fundamental" one. Moreover, there is no way to reduce the "fundamental ontology" to them without empirical input, its purely theoretical reductions are legion with no intrinsic reasons to discriminate among them. But then these rungs are emergent anyway, and point to no ideal "limit":

"The necessity, as required by the decoupling theorem and EFT, of an empirical input into the theoretical ontologies applicable at the lower energy scales - scales to which the ontologies at the higher energy scales have no direct relevance in scientific investigations - is fostering a particular representation of the physical world. In this picture the latter can be considered as layered into quasi-autonomous domains, each layer having its own ontology and associated 'fundamental' laws...
This position rejects uncompromisingly the idea successively advanced during the last fifteen years by grand unified theorists, supergravity theorists, and superstring theorists that the development of fundamental physics will end with the discovery of an ultimate, definitive, and conclusive mathematical formalism. Rather, the development is taken as a process of successive extrapolations that is assumed not to have an end..."

This suggests a different attitude to what it means to "take ontology seriously". Wallace in Everett and Structure criticizes the "fallacy of exactness" behind the hard realist readings of "real" and "exists" already in the context of quantum mechanics:

"The objection above arises from a view implicit in much discussion of Everett-style interpretations: that certain concepts and objects in quantum mechanics [like preferred basis] must either enter the theory formally in its axiomatic structure, or be regarded as illusion... To see why it is reasonable to reject the dichotomy... consider that in science there are many examples of objects which are certainly real, but which are not directly represented in the axioms. A dramatic example of such an object is the tiger: tigers are unquestionably real in any reasonable sense of the word, but they are certainly not part of the basic ontology of any physical theory."

Our ontology of everyday objects would dissolve into non-existence if we take quantum mechanics "seriously", so would classical scientific entities like chemical bonds. In quantum field theory not even quantum fields, or particles, would "exist", see Baker's Against Field Interpretations of Quantum Field Theory. Quine's indispensability approach to existence of theoretical entities seems more reasonable, in On What There Is he writes:

"The physical conceptual scheme simplifies our account of experience because of the way myriad scattered sense events come to be associated with single so-called objects; still there is no likelihood that each sentence about physical objects can actually be translated, however deviously and complexly, into the phenomenalistic language... Viewed from within the phenomenalistic
conceptual scheme, the ontologies of physical objects and mathematical objects are myths. The quality of myth, however, is relative; relative, in this case, to the epistemological point of view."

Some theoretical entities might be dispensable even from the ontological point of view. For instance, many consider virtual particles, which reify internal lines in Feynman diagrams, to be in this category, see Do we really need virtual particles to exist?, the lumeniferous ether of classical electrodynamics, once "one of the grandest generalizations of modern science" according to Michelson in 1902, is perhaps the most famous historical example.

