Order of the Tate-Shafarevich group I thought that the order of the Tate-Shafarevich group should always be a square (it's also supposed to be finite, but for the purposes of this question let's assume we know this) but I don't seem to find a good explanation; Wikipedia is silent on the matter.
While I know it may be an open problem, is there a good argument pro or contra this?
 A: Incidentally, it was thought for some time that the Brauer group $B(X)$ of a surface $X$ over a finite field could have order which was not a square.  This turned out to be false : if $B(X)$ is finite, then its order is a square (Liu--Lorenzini--Raynaud, Inventiones, 2005).  Conjecturally, the group $B(X)$ is always finite.
A: The first example of an abelian variety with nonsquare Sha was discovered in a computation by Michael Stoll in 1996.  He emailed it to me and Ed Schaefer, because his calculation depended on a paper that Ed and I had written.  At first none of us believed that it was what it was: instead we thought it must be due to either an error in Stoll's calculations or an error in the Poonen-Schaefer paper.  Stoll and I worked together over the next few weeks to develop a theory that explained the phenomenon, and this led to the paper http://math.mit.edu/~poonen/papers/sha.ps - that paper contains a detailed answer to your question.
To summarize a few of the key points: If the abelian variety over a global field $k$ has a principal polarization coming from a $k$-rational divisor (as is the case for every elliptic curve), then the order of Sha is a square (if finite), because it carries an alternating pairing - this is what Tate proved, generalizing Cassels' result for elliptic curves.  For principally polarized abelian varieties in general, the pairing satisfies the skew-symmetry condition $\langle x,y \rangle = - \langle y,x \rangle$ but not necessarily the stronger, alternating condition $\langle x,x \rangle=0$, so all one can say is that the order of Sha is either a square or twice a square (if finite).  Stoll and I gave an explicit example of a genus 2 curve over $\mathbf{Q}$ whose Jacobian had Sha isomorphic to $\mathbf{Z}/2\mathbf{Z}$ unconditionally (in particular, finiteness could be proved in this example).
If the polarization on the abelian variety is not a principal polarization, then the corresponding pairing need not be even skew-symmetric, so there is no reason to expect Sha to be even within a factor of $2$ of a square.  And indeed, William Stein eventually found explicit examples and published them in the 2004 paper cited by Simon.
A final remark: Ironically, my result with Stoll quantifying the failure of Sha to be a square is used by Liu-Lorenzini-Raynaud to prove that the Brauer group $\operatorname{Br}(X)$ of a surface over a finite field is a square (if finite)!
A: Brian Conrad told me that this is not always the case; Tate's paper where he claimed this was misunderstood until some counterexamples were found. William Stein has a paper "Shafarevich-Tate groups of nonsquare order'' with counterexamples; it's available online at http://modular.fas.harvard.edu/papers/nonsquaresha/final2.ps.
