Just wanted to +1 this. I have a client with multiple databases but only wants 1 backed up. If I use --databases=dbToBackUp, I still get all other databases' .ibd files as demonstrated in #1274766.

Additionally, different behavior is experienced during the file phase of backups (during the .frm, MYI, MYD part).  If I specify --databases=alex_and_ani_enterprise_live_new_theme, I see this:

140819 02:12:02  innobackupex: Continuing after ibbackup has suspended
140819 02:12:02  innobackupex: Executing FLUSH TABLES WITH READ LOCK...
>> log scanned up to (1286337694402)
140819 02:12:03  innobackupex: All tables locked and flushed to disk

140819 02:12:03  innobackupex: Starting to backup non-InnoDB tables and files
innobackupex: in subdirectories of '/mnt/san/mysql/mysql'
innobackupex: Backing up files '/mnt/san/mysql/mysql/alex_and_ani_enterprise_live_new_theme/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (700 files)
>> log scanned up to (1286337694402)
140819 02:12:04  innobackupex: Finished backing up non-InnoDB tables and files

140819 02:12:04  innobackupex: Executing FLUSH ENGINE LOGS...
140819 02:12:04  innobackupex: Waiting for log copying to finish

xtrabackup: The latest check point (for incremental): '1286337692872'
xtrabackup: Stopping log copying thread.
.>> log scanned up to (1286337694402)

xtrabackup: Creating suspend file '/mnt/san/backups/20140819_full/xtrabackup_log_copied' with pid '25308'
xtrabackup: Transaction log of lsn (1286331699845) to (1286337694402) was copied.
140819 02:12:05  innobackupex: All tables unlocked

==== But if I do this,  --include='^alex_and_ani_enterprise_live_new_theme\.*' I see this:

140819 09:29:05  innobackupex: Executing FLUSH TABLES WITH READ LOCK...
>> log scanned up to (1286949139524)
140819 09:29:05  innobackupex: All tables locked and flushed to disk

140819 09:29:05  innobackupex: Starting to backup non-InnoDB tables and files
innobackupex: in subdirectories of '/mnt/san/mysql/mysql'
innobackupex: Backing up files '/mnt/san/mysql/mysql/performance_schema/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (18 files)
innobackupex: Backing up files '/mnt/san/mysql/mysql/alex_and_ani_test_db/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (534 files)
innobackupex: Backing up files '/mnt/san/mysql/mysql/mysql/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (72 files)
innobackupex: Backing up files '/mnt/san/mysql/mysql/alex_and_ani_magento_loadtesting/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (700 files)
percona.checksums.frm is skipped because it does not match '^alex_and_ani_enterprise_live_new_theme\.*'.
percona.db.opt is skipped because it does not match '^alex_and_ani_enterprise_live_new_theme\.*'.
innobackupex: Backing up files '/mnt/san/mysql/mysql/alex_and_ani_wordpress_loadtesting/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (34 files)
innobackupex: Backing up files '/mnt/san/mysql/mysql/alex_and_ani_wordpress_staging/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (34 files)
innobackupex: Backing up files '/mnt/san/mysql/mysql/alex_and_ani_enterprise_live_new_theme/*.{frm,isl,MYD,MYI,MAD,MAI,MRG,TRG,TRN,ARM,ARZ,CSM,CSV,opt,par}' (700 files)
>> log scanned up to (1286949140220)
140819 09:29:07  innobackupex: Finished backing up non-InnoDB tables and files

140819 09:29:07  innobackupex: Executing FLUSH ENGINE LOGS...
140819 09:29:07  innobackupex: Waiting for log copying to finish

xtrabackup: The latest check point (for incremental): '1286948928913'
xtrabackup: Stopping log copying thread.
.>> log scanned up to (1286949140230)

xtrabackup: Creating suspend file '/mnt/san/backups/2014-08-19_09-25-23/xtrabackup_log_copied' with pid '17663'
xtrabackup: Transaction log of lsn (1286942225085) to (1286949140230) was copied.
140819 09:29:08  innobackupex: All tables unlocked

These two should be mutually exclusive and, in effect, produce the same result and similar log entries:

--databases=myDbToBackup   &&   --include='^myDbToBackup.*'