any infinite abelian group acquires some canonical non-discrete topology in this way, what is this topology?
The maximal precompact topology (used to define almost-periodic functions). See section 9.9 "Bohr topology on discrete groups" pp. 633-662 in "Topological Groups and Related Structures" by Alexander Arhangel'skii, Mikhail Tkachenko.
something like Hilbert spaces
also pre-Hilbert, or generally spaces with a (possibly even with non - symmetric orthogonality) nondegenerate sesquilinear form. (Not only in the locally convex case, or more generally for locally compact fields of scalars, but also in the Lefschetz case, i.e. duality when the skew field of scalars is discrete and in the vector spaces there is a basis at 0 of finite-codimensional subspaces).
This can be seen from many equivalent points of view: M. Pertich, Categories of algebraic systems, Springer LNM 554. (One has many crypto-equivalent definitions of structures only slightly weaker than dual pairs of vector spaces; the isomorphisms of such structures naturally correspond to proportionality classes of semi-linear isomorphisms among vector spaces). Among the many equivalent points of view, I prefer the point of view of complete irreducible DAC lattices [see F. Maeda, S. Maeda, theory of symmetric lattices], where self-duality of an object corresponds to lattice anti automorphism i.e., in classical geometric terms, a correlation of projective geometries.
(The first trick described by barcelos works in full generality, giving the "exchange" involution, corresponding to the exchange involution on a direct product ring $R\times R^{op}$ and analogoulsy for lattices; in ring and lattice theory is is considered a "degenerate" kind of involution)
Notable, somehow extreme and strange, cases: Ornstein's dual pairs (following the founding works of Mackey and Kaplansky) with some modular (but not projective or dually) subcases; Keller's orthomodular (but not Hilbert) spaces.
There is a common generalisation (of vector spaces dualities and Pontryagin - van Kampen duality) to modules over (suitable, topological) rings Flood; Orsatti, Menini, Bazzoni, \dots]. Google scholar search for "duality ring modules Pontryagin"
Morita dualities (for suitable artinian, or only perfect, rings) can be seen in this "linearly compact" context. These dualities are induced by a bimodule, which has a role like the unit circle for locally compact abelian groups or the (skew) field of scalars for vector spaces.
One can consider also dualities between more general abelian categories of modules; in this context I like the WQF (weakly quasi Frobenius) a.k.a. IF (injectives are flat) rings, i.e. the coherent rings such that the usual dual (Hom to the ring of scalars) gives a duality of the abelian categories of finitely presented right and left modules. This can be seen equivalently in terms of Hutchinson (modular) lattices of the abelian categories; WQF rings such that intervals in this lattice are complemented (resp. noetherian or artininan or finite length) are exactly the von Neumann regular rings (resp. quasi-Frobenius rings).
[Note that in these last cases no topology is used, since all considered modules are finitely presented: in these (and the following) algebraic contexts, topology only usefully appears when also infinite direct products, or dually sums, make sense; then these topologies are 0-dimensional, being subspaces of infinite direct products of discrete spaces (the algebraic object that induces the duality, and that need not be self-dual, has a discrete topology in purely algebraic contexts). Analogously, in the theory of field extensions, a topology usefully appears in the Galois group only for infinite extensions, and the group is pro-finite]
What is the topology on a distributive lattice $L$ induced from the embedding $L\hookrightarrow 2^{\textrm{prime filters of }L}$? Or is it more appropriate to consider the topology induced from the Vietoris space of the dual? Or are these actually the same?
Homomorphisms to $\{0,1\}$ (prime ideals are their kernels) i.e. dispersion free (finitely additive probability) measures i.e. extreme points of the compact convex set of (finitely additive probability) measures are the same for a distributive lattice and its freely generated Boolean algebra. This explains why in Priestley representation inside a compact T$_2$ space (the above extreme points, closed subset of the compact convex set and generating it in the Krein - Millman way) one needs additional structure (the specialisation order, coming from the original T$_0$ spectral space of Stone, which is crypto - equivalent to the totally order disconnected T$_2$ compact space: the Stone advantage is that no extra-topological structure is needed, the disadvantage is that is is not T$_2$ in the non Boolean case).
In the Boolean case, a variable clopen weakly converges (in this duality with measures, or even only the delta measures) to a fixed clopen iff it has eventually the same points (in the Stone space); it is the same as the convergence induced on clopen sets by the Vietoris topology on the space of closed sets of the compact T$_2$ space (may "hyperspace" topologies are known and useful for topological spaces, but for compact metrisable spaces they all coincide). For sequences, you see the traditional LimInf and LimSup of sequences of sets, and generally one of the traditional intrinsic topologies in a ordered set (see below).
the self-dual category of complete join-semilattices, but here also I do not understand why has topology disappeared altogether.
Various convergences (and topologies) are natural and useful in complete lattices: see Birkoff's book and the compendium of continuous lattices and its successor book (also partially useful in the context of these dualities). [Warning: except the completely distributive case (complete sub lattices of direct products of complete chains), some of the important natural convergences are not topological.] They do not disappear, but they are implicit and more than one.
things like Stone, Priestley and Esakia dualities
In general: natural dualities (Davey). Google scholar search with "Pontryagin Priestley duality" gives useful introductions to
the subject, such as http://www.researchgate.net/publication/242014244_Duality_Theory_on_Ten_Dollars_a_Day/file/60b7d51cba47a1d37e.pdf
In what sense may one speak of self-dual objects in context of Priestley and other Stone-like dualities? Is there any self-dual category at all either including or included in both Priestley spaces and distributive lattices?
in many cases, possibly almost none. See below.
What about Gelfand duality in this context?
Yes, it is included [in terms of probability measures these are the Radon measures, the Dirac's deltas being the extreme points, the compact convex set being the unit ball in the weak topology of the duality. This way of looking at the duality extends to the non commutative case: looking at homomorphisms to the ring of scalars is insufficient in the general case, and using representations in Hilbert spaces gives various notions of "points" (equivalence classes of suitable representations): the above ones, via GNS representation; the primitive spectrum; the closed prime spectrum]
The Gelfand case (which includes Stone duality) is a typical case that shows how little sense can sometimes have a hunt for self-duality in this context: on one side of the duality one has (suitable, complete, semiprimitive, commutative) normed algebras; on the other side one has locally compact spaces, and a normed space is locally compact iff finite dimensional, which for complex commutative semiprimitive algebras means finite direct product of copies of the complex field, so its dual is a finite discrete space, so it cannot be a complex algebra (unless 0).
what are those Priestley spaces $(X,\leqslant)$ which happen to be distributive lattices with respect to $\leqslant$?
Here I consider only the Priestley space of finite distributive lattices (but algebraic dually algebraic distributive lattices can be treated in the same way). Here Priestley duality, once restated as spectral duality (the original form by Stone), reduces to the Birkhoff transform: the equivalence between finite posets, finite T$_0$ (topological, even T$_D$ and sober) spaces, finite distributive lattices. [The poset is the poset of join-irreducible elements of the lattice; the order on the poset is the specialisation order of the topology and the subposet order from the lattice; the lattice is the lattice of closed sets of the spectral topology, the points are the dense points of the irreducible closed sets]. So you have (finite) distributive lattices which are the lattices of all order ideals in a (finite) distributive lattice. No Boolean algebras except $\{0,1\}$ (and $0=1$) are of this form, since (complete atomic) Boolean algebras are the distributive lattices that in Birkhoff transform correspond to posets that are antichains. Generally, no self-dual object is obtained except finite chains, since chains are exactly the distributive lattices where each element is join-irreducible.
Finite chains are so special than it is perhaps better to look at them not simply as distributive lattices, but as more structured objects: as truth values generalising $0,1$ one looks at them as Post algebras, then Chang MV algebras (equivalently, by Mundici's equivalence, as unit intervals in lattice ordered abelian groups with fixed strong unit). As lattices, the natural "noncommutative" generalisation of finite chains are semiprimary lattices (someone instead likes Elliott's theorem that two AF $C^*$-algebras with a natural lattice order on dimensions [the Murray - von Neumann classes of projections] are isomorphic iff the associated MV algebras of dimensions are isomorphic. However, this theorem is not a equivalence: no natural composition preserving bijection is given for isomorphisms on the two sides). These very special modular lattices of finite length were studied by Baer, Inaba, J\'onsson - Monk culminating in their coordinatization theorem (in the primary decomposable case).
The typical examples of primary decomposable lattices are: lattice of subgroups of finite abelian groups (including the theory of elementary divisors of a matrix with integer entries); lattice of invariant subspaces for a single semi-linear endomorphisms of a finite dimensional vector space (including rational and Jordan form of matrices over fields); more generally, lattices of all submodules of finitely generated modules over artinian principal ideal rings (including all torsion finitely generated modules over principal ideal domains and Dedekind domains, since any proper homomorphic image of these is an artinian principal ideal ring). In terms of the Hutchinson lattice as above, the artinian rings such as the Hutchinson lattice of the abelian category of finitely generated modules has semiprimary (resp. primary decomposable) intervals are exactly the artinian serial rings (resp. artinian principal ideal rings); the abelian categories of right and left finitely generated modules are then in Morita duality (but a dualizing bimodule is the ring of scalars only in the quasi Frobenius case, which includes the principal ideals case but not every serial case). [There is also a theory for finitely presented modules over non artinian serial rings, including all discrete valuation domains, and even generic valuation domains; also related: every proper homomorphic image of a Pr\"ufer domain is a WQF ring]
If there are cases of "natural dualities" where a self-duality is known and useful, Davey et. al. should have them. Perhaps start with Theorem 3.15 (The Strong Self-Duality Theorem) in the "ten dollars" survey cited above, then consider endodualisability
But it seems to me that the most useful path to find self-dualities is in the "analytic" Pontryagin vein (incidentally, Hopf algebras appear when dualizing locally compact noncompact nonabelian groups), not in the "algebraic" Stone vein.