Ubuntu:

Do you want to set by default repair file systems with inconsistencies
during boot time will never pause and asking any questions.

Open the file /etc/default/rcS

## automatically repair filesystems with inconsistencies during boot
FSCKFIX=no

By default the FSCKFIX is disable (no), so just change the line to enable(yes),
 
FSCKFIX=yes

save a file and reboot. Another way is just to create a file and reboot the system,
 
# touch /forcefsck
# shutdown -r now

CentOS:

File system checks while booting in CentOS for force fsck on next booting,
 
#  shutdown -r -F

-r for rebooting system  and
-F Force fsck on reboot.

Do you require to run fsck  when every rebooting system, make a file and insert the trace lines,
 
# vi /etc/sysconfig/autofsck

AUTOFSCK_TIMEOUT=5
AUTOFSCK_DEF_CHECK=yes

or just create a file and reboot the system,
 
# touch /forcefsck

# shutdown -r now