Question: Here's a question that I've wondered about somewhat idly from time to time.
I think it would be hard, but even a partial result would be interesting.
Hopefully someone here can make some headway.

Fix an algebraically closed field k (one can also relax this, e.g. k = $\mathbb{Q}$
is very interesting). Suppose that X and Y are two closed subschemes of affine or projective spaces over k given by explicit equations.

*Is there an algorithm to decide whether X and Y are isomorphic?*

A few comments.

1. I'm being a bit sloppy about the use of the word "algorithm". One can assume that the operations of k are Turing computable, or else choose a different model of computation.
2. For affine schemes, this can be stated as the isomorphism problem for finitely generated
commutative k-algebras. I expect that the isomorphism problem for noncommutative finitely presented associative algebras would be false, since it seems close to the corresponding problem for groups which is undecidable. But the reduction is not quite clear to me. Is this known?
3. To give a positive solution, one would need an effective threshold d, so that either
there is no isomorphism at all or there exists an isomorphism defined by a rational expression with degree (of the numerator and denominator) bounded by $d$. I have no
feeling for whether this reasonable or not.
4. For the simplest case, where X is a smooth projective plane curve, a positive
solution would amount showing that the corresponding point in the moduli space $M\_g$, is
computable ($g= (deg X-1)(deg X-2)/2$ ). This looks challenging, but somehow it feels tractable to me.

Added Note: While I think spontaneous discussion is good, I would like to encourage
anyone who has a substantial result about this to write it down carefully and perhaps post it on the arxiv.

Answer: 
Those are very nice questions. In fact, I too have been asking these questions: see the last few slides in [this file](http://www-math.mit.edu/~poonen/slides/cantrell3.pdf).
Here are a few comments.

2) If you had an algorithm to decide isomorphism of finitely presented noncommutative $k$-algebras, applying it to group algebras $kG$ associated to finitely presented groups $G$ would let you decide whether a finitely presented group is trivial, but that is a well-known undecidable problem. So this isomorphism problem is undecidable.

4) To decide whether two smooth projective curves over $\overline{\mathbb{Q}}$ are isomorphic, first compute the genus of each curve. Assume that they are the same, both equal to $g$. If $g=0$, they are isomorphic. If $g=1$, compute Weierstrass models and then $j$-invariants. If $g \ge 2$, compute tricanonical embeddings (i.e., associated to the linear system $|3K|$), and try to solve the equation that says that a linear automorphism of the ambient projective space sends one curve to the other. This solves the problem for curves. An extension of this idea solves the problem in higher dimensions whenever one of the varieties is of general type. (I think this was first observed by Burt Totaro.)

As far as I know, all your other questions are open. In particular, it is not clear whether one can relate them to Hilbert's tenth problem over $\mathbb{Z}$ or $\mathbb{Q}$ (or to undecidable problems like the word problem for finitely presented groups).
It seems that one can embed 10th Hilbert problem over $\mathbb Z$ into this question, and for that the answer is not known.