During normal operations, only use the repairDatabase command and wrappers including db.repairDatabase() in the mongo shell and mongod --repair, to compact database files and/or reclaim disk space. Be aware that these operations remove and do not save any corrupt data during the repair process.
If you are trying to repair a replica set member, and you have access to an intact copy of your data (e.g. a recent backup or an intact member of the replica set), you should restore from that intact copy, and not use repairDatabase.
db.repairDatabase() provides a wrapper around the database command repairDatabase, and has the same effect as the run-time option mongod --repair option, limited to only the current database. See repairDatabase for full documentation.