I have just installed Meteor version 0.5.9 (45fef52095) to my CentOS release 6.3 (Final) server (Linux version 2.6.32-279.19.1.el6.i686 (mockbuild@c6b8.bsys.dev.centos.org)
If you have installed Mongo globally, then be sure to delete all the prealloc files in the /db/journal folder.
For Ubuntu, the /db/ folder is normally located in /data so the full path is /data/db/journal. This might be different for other OS's.