When running a 3 node replSet with lots of data and currently and have more than 1500 datafiles, you got the following error messages at restart.
It looks like it has something to do with a FD_SETSIZE limitation to 1024. But ulimit -n is set correctly (ulimit -n 550000).

This bug might correspond to https://jira.mongodb.org/browse/SERVER-8515

Version 2.4.3

Thu May 30 15:57:27.912 [initandlisten] db version v2.4.3
Thu May 30 15:57:27.912 [initandlisten] git version: fe1743177a5ea03e91e0052fb5e2cb2945f6d95f
Thu May 30 15:57:27.912 [initandlisten] allocator: tcmalloc
Thu May 30 15:57:27.912 [initandlisten] options:

{ config: "/etc/mongod-longterm.conf", dbpath: "/data/mongo-longterm", fork: "true", logappend: "true", logpath: "/var/log/mongo/mongod-longterm.log", pidfilepath: "/var/run/mongodb/mongod-longterm.pid", port: 30001, replSet: "rs-longterm" }

Thu May 30 15:57:27.937 [initandlisten] journal dir=/data/mongo-longterm/journal
Thu May 30 15:57:27.938 [initandlisten] recover : no journal files present, no recovery needed
Thu May 30 15:57:43.596 [websvr] ERROR: socket 1201 is higher than 1023; not supported
Thu May 30 15:57:43.596 [initandlisten] ERROR: socket 1200 is higher than 1023; not supported
Thu May 30 15:57:43.597 [initandlisten] now exiting
Thu May 30 15:57:43.597 dbexit:
Thu May 30 15:57:43.597 [initandlisten] shutdown: going to close listening sockets...
Thu May 30 15:57:43.597 [initandlisten] closing listening socket: 1199
Thu May 30 15:57:43.597 [initandlisten] closing listening socket: 1200
Thu May 30 15:57:43.597 [initandlisten] closing listening socket: 1201

--------------------------------

Version 2.5.1-pre from github

Thu May 30 15:58:30.605 [initandlisten] db version v2.5.1-pre-
Thu May 30 15:58:30.605 [initandlisten] git version: 3b1257a5224d1e9df71ee1b4631ca32f2cf438f2
Thu May 30 15:58:30.605 [initandlisten] allocator: tcmalloc
Thu May 30 15:58:30.605 [initandlisten] options:

{ config: "/etc/mongod-longterm.conf", dbpath: "/data/mongo-longterm", fork: "true", logappend: "true", logpath: "/var/log/mongo/mongod-longterm.log", pidfilepath: "/var/run/mongodb/mongod-longterm.pid", port: 30001, replSet: "rs-longterm" }

Thu May 30 15:58:30.633 [initandlisten] journal dir=/data/mongo-longterm/journal
Thu May 30 15:58:30.633 [initandlisten] recover : no journal files present, no recovery needed
Thu May 30 15:58:30.923 [initandlisten] ERROR: socket 1201 is higher than 1023; not supported
Thu May 30 15:58:30.926 [initandlisten] now exiting
Thu May 30 15:58:30.926 [IndexRebuilder] assertion 11600 interrupted at shutdown ns:local.system.namespaces query:{}
Thu May 30 15:58:30.926 dbexit:
Thu May 30 15:58:30.926 [initandlisten] shutdown: going to close listening sockets...
Thu May 30 15:58:30.926 [initandlisten] closing listening socket: 1200
Thu May 30 15:58:30.926 [IndexRebuilder] warning: index rebuilding did not complete
Thu May 30 15:58:30.926 [initandlisten] closing listening socket: 1201