Which command would you use to run a defrag on a Exchange mail store ?

See Microsoft Support: How to defragment Exchange databases.

Scleros's answer points you to the exact utility you will need to use for an OFFLINE defragmentation and points you to information for an ONLINE defragmentation. There are slight variations of the ESEUTIL utility depending on the version and service pack level of Exchange you are using.

Depending on how heavily your information stores are used and how large they are, OFFLINE fragmentation may be performed anywhere from 2 to 6 month intervals.

If your IS gets unruly, then consider splitting it up into multiple Information Stores. If we did not employ automated archival and did not have it split up into eight IS's, the one at our HQ location would be about 1.5TB in size.

The larger it is, the longer the OFFLLINE defragmentation takes and the longer your users are without access to their email. It is best performed after a backup since a FULL backup will commit the log files and clean them up (unless you are using Circular Logging - bad idea).

Perform a Soft Recovery to commit the log files prior to a defrag of the IS.

Chuck.
11 years as Exchange admin.