Sybase:
before 12.5: buildmaster (bldmatr for NT)
buildmaster -d master_device -s size_in_2k_pages

12.5 and later: dataserver with some options (sqlsvr for NT)
dataserver -d master_device -b size -forcebuild -z page_size -Z size_of_master_db

MS SQL:

before MS 2005:
rebuildm utility (GUI)

MS SQL 2005:

1. Start server in single-user mode (sqlserver.exe -m)
2. setup.exe /qn INSTANCENAME=instance_name REINSTALL=SQL_Engine REBUILDDATABASE=1 SAPWD=new_SA_Password
3. Restart server in normal mode