We're currently shipping with memory mapped lucene implementation as the default due to an issue which affects Windows users:
http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=6265734
This implementation can cause excessive virtual memory space to be consumed in large instances.
According to the issue above the problem does not exist in Java 7. Since we will be requiring Java 7 to run Nexus as of version 2.6 we should now make NIO implementation the default.