When I apply my custom indexes or missing indexes, I put _fmcb_ in the name of the index. This way, I can run the below query and extract all of them out for a separate build script.

http://social.technet.microsoft.com/wiki/contents/articles/19598.how-to-generate-index-creation-scripts-for-all-tables-in-a-database-using-t-sql.aspx

SELECT  ' CREATE ' +
 CASE WHEN I.is_unique = 1 THEN ' UNIQUE ' ELSE '' END  +
 I.type_desc COLLATE DATABASE_DEFAULT +' INDEX ' +
 I.name  + ' ON '  +
 Schema_name(T.Schema_id)+'.'+T.name + ' ( ' +
 KeyColumns + ' )  ' +
 ISNULL(' INCLUDE ('+IncludedColumns+' ) ','') +
 ISNULL(' WHERE  '+I.Filter_definition,'') + ' WITH ( MAXDOP=0, ' +
 CASE WHEN I.is_padded = 1 THEN ' PAD_INDEX = ON ' ELSE ' PAD_INDEX = OFF ' END + ','  +
 'FILLFACTOR = '+CONVERT(CHAR(5),CASE WHEN I.Fill_factor = 0 THEN 100 ELSE I.Fill_factor END) + ','  +
 -- default value
 'SORT_IN_TEMPDB = OFF '  + ','  +
 CASE WHEN I.ignore_dup_key = 1 THEN ' IGNORE_DUP_KEY = ON ' ELSE ' IGNORE_DUP_KEY = OFF ' END + ','  +
 CASE WHEN ST.no_recompute = 0 THEN ' STATISTICS_NORECOMPUTE = OFF ' ELSE ' STATISTICS_NORECOMPUTE = ON ' END + ','  +
 -- default value
 ' DROP_EXISTING = ON '  + ','  +
 -- default value
 ' ONLINE = OFF '  + ','  +
 CASE WHEN I.allow_row_locks = 1 THEN ' ALLOW_ROW_LOCKS = ON ' ELSE ' ALLOW_ROW_LOCKS = OFF ' END + ','  +
 CASE WHEN I.allow_page_locks = 1 THEN ' ALLOW_PAGE_LOCKS = ON ' ELSE ' ALLOW_PAGE_LOCKS = OFF ' END  + ' ) ON [' +
 DS.name + ' ] '  [CreateIndexScript]
 FROM sys.indexes I
 JOIN sys.tables T ON T.Object_id = I.Object_id
 JOIN sys.sysindexes SI ON I.Object_id = SI.id AND I.index_id = SI.indid
 JOIN (SELECT * FROM (
 SELECT IC2.object_id , IC2.index_id ,
 STUFF((SELECT ' , ' + C.name + CASE WHEN MAX(CONVERT(INT,IC1.is_descending_key)) = 1 THEN ' DESC ' ELSE ' ASC ' END
 FROM sys.index_columns IC1
 JOIN Sys.columns C
 ON C.object_id = IC1.object_id
 AND C.column_id = IC1.column_id
 AND IC1.is_included_column = 0
 WHERE IC1.object_id = IC2.object_id
 AND IC1.index_id = IC2.index_id
 GROUP BY IC1.object_id,C.name,index_id
 ORDER BY MAX(IC1.key_ordinal)
 FOR XML PATH('')), 1, 2, '') KeyColumns
 FROM sys.index_columns IC2
 --WHERE IC2.Object_id = object_id('Person.Address') --Comment for all tables
 GROUP BY IC2.object_id ,IC2.index_id) tmp3 )tmp4
 ON I.object_id = tmp4.object_id AND I.Index_id = tmp4.index_id
 JOIN sys.stats ST ON ST.object_id = I.object_id AND ST.stats_id = I.index_id
 JOIN sys.data_spaces DS ON I.data_space_id=DS.data_space_id
 JOIN sys.filegroups FG ON I.data_space_id=FG.data_space_id
 LEFT JOIN (SELECT * FROM (
 SELECT IC2.object_id , IC2.index_id ,
 STUFF((SELECT ' , ' + C.name
 FROM sys.index_columns IC1
 JOIN Sys.columns C
 ON C.object_id = IC1.object_id
 AND C.column_id = IC1.column_id
 AND IC1.is_included_column = 1
 WHERE IC1.object_id = IC2.object_id
 AND IC1.index_id = IC2.index_id
 GROUP BY IC1.object_id,C.name,index_id
 FOR XML PATH('')), 1, 2, '') IncludedColumns
 FROM sys.index_columns IC2
 --WHERE IC2.Object_id = object_id('Person.Address') --Comment for all tables
 GROUP BY IC2.object_id ,IC2.index_id) tmp1
 WHERE IncludedColumns IS NOT NULL ) tmp2
 ON tmp2.object_id = I.object_id AND tmp2.index_id = I.index_id
 WHERE i.name like '%fmcb%'
 --I.is_primary_key = 0 AND I.is_unique_constraint = 0
 --AND I.Object_id = object_id('Person.Address') --Comment for all tables
 -- AND I.name = 'IX_Address_PostalCode' --comment for all indexes