Let $X_1, \ldots, X_n$ be a collection of random variables. Consider the directed graph with vertex set $\{ 1, 2, \ldots, n \}$ where there is a directed edge $i \to j$ if $\mathbb{P}(X_i > X_j) > \frac{1}{2}$.
Question 1: What directed graphs can arise in this way? Certainly they must be simple and have no loops. Is that the only restriction? Alternatively, $\mathbb{P}(X_i > X_j) > \frac{1}{2}$ defines an irreflexive antisymmetric relation on $\{ 1, 2, ... n \}$. Which such relations arise in this way?
Question 2: Does the answer change if we require the $X_i$ to all be defined on a finite sample space?
Question 3: What if we require the $X_i$ to be independent?
It is known (see nontransitive dice) that this graph can have directed cycles even if the $X_i$ are independent; in particular, the corresponding relation need not be transitive.
Note: I wrote this answer before question 3 became a separate part of the question; this answer only answers questions 1 and 2. Question 3 seems harder.
Every simple directed graph arises in this way. Consider probability distributions over all $n!$ possible total orders of the values of the $X_i$, and associate a potential directed edge $i\to j$ with the distribution that has probability zero for orders with $X_i\lt X_j$ and $2/n!$ for orders with $X_i\gt X_j$. Given a directed graph, choose any network flow with positive flow along all the directed edges (you can always find one by taking any flow from the sources to the sinks and adding circular flow to the cycles if necessary), and form the normalized linear combination of the distributions associated with the edges, with coefficients given by the flow.
Now consider an edge $i\to j$. The contributions from any edges not incident at $i$ or $j$ don't affect whether $\mathbb P(X_i\gt X_j)\gt\frac12$, since they assign weight to equally many orders with $X_i\gt X_j$ as with $X_i\lt X_j$. Thus we only need to consider edges incident at $i$ or $j$. For an edge $j\to k$, consider the six possible orders of $X_i$, $X_j$ and $X_k$. Three of these are assigned weight by the edge $j\to k$, namely $X_i\gt X_j\gt X_k$, $X_j\gt X_i\gt X_k$ and $X_j\gt X_k\gt X_i$, and of these, one has $X_i\gt X_j$ and two have $X_i\lt X_j$. For an edge $k\to j$, it's the other way around.
Thus, considering the effect of all edges on $\mathbb P(X_i\gt X_j)-\frac12$, the edge $i\to j$ itself contributes $1-\frac12=\frac12$, edges not incident at $i$ or $j$ contribute $\frac12-\frac12=0$, edges "aligned with" $i\to j$, of the forms $k\to j$ and $i\to k$, contribute $\frac23-\frac12=\frac16$, and edges "opposed to" $i\to j$, of the forms $j\to k$ and $k\to i$, contribute $\frac13-\frac12=-\frac16$. Equal but opposite contributions from "aligned" and "opposed" edges cancel, so for a non-terminal edge the net result is equivalent by flow conservation to that of one incoming "opposed" edge incident at $i$ and one outgoing "opposed" edge incident at $j$ with net flows equal to that of $i\to j$. Thus the net result is that flow times $\frac12-\frac16-\frac16=\frac16\gt0$. The situation is only improved by sources and sinks.
If neither $i\to j$ nor $j\to i$ is an edge in the graph, then if $i$ and $j$ are not sources or sinks all contributions cancel and $\mathbb P(X_i\gt X_j)=\frac12\not\gt\frac12$ as desired; and again the situation is only improved by sources and sinks.
Qiaochu, I should add that I probably wouldn't have come up with this solution if I hadn't learned from you to try to reduce everything to linear algebra. :-)