The use of embedding a curve into its Jacobian I'm looking for as many examples/applications as possible of the use of embedding a smooth projective geometrically connected curve $X$ over a number field $k$ with $X(k)\neq \emptyset$ into its Jacobian (via a rational point). Please do not take the meaning of "use" to seriously.  
I know of 
Chabauty's method of proving a special case of the Mordell conjecture.
Faltings' use of the Torelli map in his proof of the Shafarevich conjecture for curves.
Raynaud's theorem (previously Manin-Mumford conjecture).
The Bogomologov conjecture (proven by Ullmo and Zhang).
The Mordell-Lang theorem.
In some of these examples the embedding of X into its Jacobian is simply part of the statement. I also consider this as "useful".
Are there any other nice examples? They don't have to be as difficult as the ones mentioned above.
 A: Another use of embedding a curve into its Jacobian is to apply the `Mordell-Weil Sieve'. Suppose $k = \mathbb Q$ for simplicity and that you don't know a rational point on $X$, but you know a rational divisor (class) $D$ of degree 1 on $X$. Then you can use $D$ to define an embedding $\iota$ of $X$ into its Jacobian $J$. Now assume in addition that $J(\mathbb Q)$ is known explicitly. Then for every prime $p$ (of good reduction, say), you can consider the images of $X(\mathbb F_p)$ and of $J(\mathbb Q)$ in $J(\mathbb F_p)$ (the first under $\iota$, the second by reduction mod $p$). Clearly, $X(\mathbb Q)$ has to map into the intersection of these two. Now instead of considering one prime, we can consider all primes in a finite set $S$ and look at the product of $\iota(X(\mathbb F_p))$ over all $p \in S$ and the image of $J(\mathbb Q)$ in the product of $J(\mathbb F_p)$ over all $p \in S$.
Now for a suitable choice of $S$ it may be the case that the two sets are disjoint, which then proves that $X$ has no rational points. There are good reasons to believe that it is always possible to prove that $X({\mathbb Q})$ is empty in this way (if it is empty). See this paper.
A: You could also mention Vojta's proof of Mordell conjecture, as well as its generalization by Faltings (the proof of the so-called Mordell-Lang conjecture) and its simplification by Bombieri (Mordell conjecture revisited).
Faltings's presentation is explicitly about subvarieties of Abelian varieties.
In the presentation by Vojta-Bombieri, you work on a power of a curve and prove a certain height inequality; you then need to interprete this within the Jacobian, as a lower bound for the angle made (in the Mordell-Weil lattice) by two points of the curve.
A: In the section conjecture for a number field $k$: the proof of the injectivity of the map
$$X(k)\to \mathrm{HomExt}_{G_k}(G_k,\pi_1(X,\overline{x}))$$
that attributes to a rational point a section of the fundamental exact sequence
$$ 1\to \pi_1(\overline{X},\overline{x})) \to \pi_1(X,\overline{x})\to G_k \to 1 $$
uses an embedding of $X$ into its jacobian to reduce to an abelian variety $A$. The map above is then interpreted as limit of coboundary maps in étale cohomology for the Kummer exact sequences for $A$. One applies Mordell-Weil theorem ($A(k)$ is an abelian group of finite type) to conclude.
See 
Jakob Stix
On cuspidal sections of algebraic fundamental groups 
http://arxiv.org/abs/0809.0017
appendix B
for details. This was known to Grothendieck back in 1983, see 
Grothendieck, Alexander
Brief an G. Faltings. (German) [Letter to G. Faltings] 
http://www.math.jussieu.fr/~leila/grothendieckcircle/GtoF.pdf
A: This is not really about the embedding, rather about the identification of points on the Jacobian with degree-0-divisors.
If you are given a cuspidal form $f\in S_2(\Gamma_0(N),\mathbb{Q})$, by definition you have a differential form on $X_0(11)$. In order to say that there is an elliptic curve corresponding to $f$ (Shimura-Taniyama-Weil conjecture – and Wiles proves – that every elliptic curve arises in this way, but the direction I am discussing is much older) you want to find a quotient of $J_0(N)=\mathrm{Jac}(X_0(N))$ corresponding to $f$ and to do this you need to transfer the action of endomorphisms of modular forms (i.e. of diferentials) to endomorphisms of the Jacobian. In this way you find an ideal $I_f\subseteq \mathrm{End}(J_0(N))$ such that the corresponding quotient $J_0(N)/I_f$ is the elliptic curve $E_f$. The way one ''transfers the action of endomorphisms of differentials on $X_0(N)$ to endomorphisms of $J_0(N)$'' is through the embedding $X_0(N)\hookrightarrow J_0(N)$. Much of what I said can be generalized to forms of weight $k\geq 2$.
A: One can deduce the Weil conjectures for curves from the case of Abelian varieties. (See Milne's Abelian Varieties lecture notes http://jmilne.org/math/CourseNotes/AV.pdf section 11 or his article in Cornell-Silverman.)
