The "Computational Science" and "Computer Science" Stack Exchange sites have the same exact logo ("CS" in a blue speech balloon). Cryptography and Code Review do as well ("CR" in a blue speech balloon). This is bad for bookmarks, especially when one identifies them only by their logo. This should be remedied, especially since they cover similar topics.
This will probably crop up more and more often as SE plods on. As Ephraim noted, Codereview and Cryptography also have the same logo.
Though out here, Cryptography is
CR(as per favicon). A similar thing with Economics (inconsistency, anyone?), and many other sites.
Stuff I can think of
Do some nifty capitalization.
Add an extra letter, like Cognitive Sciences (
Note that these sites are in beta for just
a few months^6-8 weeks, then they get their own logos.