Assuming you have a master DB backup, it can be restored, but the process is cumbersome, not well documented, and differs slightly depending on which version of SQL you're using. SQL 2008 R2 is slightly different than SQL 2008.

Essentially it is

1) Launching a file in the MSSQL folder that will recreate the system databases. You may want to move/rename the msdb and model data and log files so they don't get overwritten. This will allow SQL Service to start, but it will not recognize the user databases.

2) Configure SQL to start in Single User mode. Open the SQL command line interface, then run a RESTORE DATABASE command to restore the master database from your master db backup (assuming you have one). You can't do this from Management Studio because that maintains a connection to master, and you can't restore and DB if there is another connection to the DB.

3) When the restore completes, the SQL service will shut down. Reconfigure for multiuser access. Restore/fix the other system DBs and you should be good to go.

Please google with the exact version of SQL to get the details of the process I've outlined.

To prevent this, during downtimes I periodically place a copy of master.mdf into a folder on the C drive. If you've done this after updates, config changes and adding/dropping DBs you may be able to skip steps 1-3 above.