When looking closely at some set arithmetic, I realized that all of the three symbols in the following minimum example are rendered here (pdfLaTeX on Portable MiKTeX, Windows 7 x64) at different vertical positions:
\documentclass{article}
\begin{document}
$x \in X$
\end{document}
Magnified screenshot, when viewed in Adobe Acrobat Pro 9 (added red line manually):

The question: (why) is this as it should be? My naive view would expect at least $x$ and $X$ to share the same baseline.

oandO) cross the baseline a bit. This is done to make them look like they rest on the same baseline as do the characters with hard lower edges (such as B, D, E, L, Z, and a few more). – Mico Oct 21 '13 at 18:09