I got that nasty error after moving around different directories in /var/lib/mysql:
root@server:/var/lib/mysql# /etc/init.d/mysql start
Starting MySQL. ERROR! Manager of pid-file quit without updating file.
There were all kind of suggestions about it on the net, most of which had something to do with incorrect shutdown or incorrect permissions for the pid file.
One of the suggestions reminded me to read the mysql error log 
Here is what the error log said:
root@server:/var/lib/mysql# /etc/init.d/mysql start
Starting MySQL. ERROR! Manager of pid-file quit without updating file.
root@server:/var/lib/mysql# mysql
mysql mysql_config mysqldumpslow mysql_idle_processes.pm mysqlshow mysql_tzinfo_to_sql
mysqlaccess mysql_convert_table_format mysql_explain_log mysqlimport mysql_sock.pm mysql_upgrade
mysqladmin mysqld mysql_find_rows mysql_install_db mysql_tableinfo mysql_upgrade_shell
mysqlbinlog mysqld-debug mysql_fix_extensions mysql_logs.sh mysqltest mysql_waitpid
mysqlbug mysqld_multi mysql_fix_privilege_tables mysqlmanager mysqltestmanager mysql_zap
mysqlcheck mysqld_safe mysqlhotcopy mysql_secure_installation mysqltestmanagerc
mysql_client_test mysqldump mysqlhotcopy.orig mysql_setpermission mysqltestmanager-pwgen
root@server:/var/lib/mysql# mysqld
mysqld mysqld-debug mysqld_multi mysqld_safe mysqldump mysqldumpslow
root@server:/var/lib/mysql# mysqld
mysqld mysqld-debug mysqld_multi mysqld_safe mysqldump mysqldumpslow
root@server:/var/lib/mysql# mysqld_safe start
Starting mysqld daemon with databases from /var/lib/mysql
STOPPING server from pid file /var/lib/mysql/host.server.bgsnow.com.pid
091114 13:14:56 mysqld ended
root@server:/var/lib/mysql# ll /var/lib/mysql/host.server.bgsnow.com.p
root@server:/var/lib/mysql# touch /var/lib/mysql/host.server.bgsnow.com.pid
root@server:/var/lib/mysql# chown mysql: /var/lib/mysql/host.server.bgsnow.com.pid
root@server:/var/lib/mysql# /etc/init.d/mysql start
Starting MySQL. ERROR! Manager of pid-file quit without updating file.
root@server:/var/lib/mysql# tail -f /var/lib/mysql
mysql/ mysqlA/ mysqlOLD/
root@server:/var/lib/mysql# tail -f /var/lib/mysql/mysql-slow.log
host.server.bgsnow.com.err ib_logfile0 mysql-slow.log optistr2_optistreams/
ibdata1 ib_logfile1 optistr2_opti/ optistr2_perldesk/
root@server:/var/lib/mysql# tail -f /var/lib/mysql/host.server.bgsnow.com.err
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 0 43655
091114 13:16:20 InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
091114 13:16:21 InnoDB: Started; log sequence number 0 43655
091114 13:16:21 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
091114 13:16:21 mysqld ended
091114 13:16:52 mysqld started
InnoDB: Log scan progressed past the checkpoint lsn 0 36808
091114 13:16:52 InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 0 43655
091114 13:16:52 InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
091114 13:16:53 InnoDB: Started; log sequence number 0 43655
091114 13:16:53 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
091114 13:16:53 mysqld ended
root@server:/var/lib/mysql# ls
./ ../ host.server.bgsnow.com.err ibdata1 ib_logfile0 ib_logfile1 mysql-slow.log optistr2_opti/ optistr2_optistreams/ optistr2_perldesk/
root@server:/var/lib/mysql# ll ../
alternatives/ dhclient/ logrotate.status mlocate/ mysqlA/ pgsql/ rkhunter/ sepolgen/ stateless/ yum/
dbus/ games/ misc/ mysql/ mysqlOLD/ random-seed rpm/ spamassassin/ texmf/
root@server:/var/lib/mysql# ll ../
alternatives/ dhclient/ logrotate.status mlocate/ mysqlA/ pgsql/ rkhunter/ sepolgen/ stateless/ yum/
dbus/ games/ misc/ mysql/ mysqlOLD/ random-seed rpm/ spamassassin/ texmf/
root@server:/var/lib/mysql# ll ../mysqlOLD/
cphulkd/ host.server.bgsnow.com.err ib_logfile0 mysql/ roundcube/ sentry_stat/
eximstats/ host.server.bgsnow.com.pid ib_logfile1 mysql-slow.log sentry/ sentry_traf/
horde/ ibdata1 leechprotect/ mysql.sock sentry_mambo/ test/
root@server:/var/lib/mysql# ll ../mysqlOLD/*
root@server:/var/lib/mysql# ls
./ ../ host.server.bgsnow.com.err ibdata1 ib_logfile0 ib_logfile1 mysql-slow.log optistr2_opti/ optistr2_optistreams/ optistr2_perldesk/
root@server:/var/lib/mysql# mv ../mysqlOLD/
cphulkd/ host.server.bgsnow.com.err ib_logfile0 mysql/ roundcube/ sentry_stat/
eximstats/ host.server.bgsnow.com.pid ib_logfile1 mysql-slow.log sentry/ sentry_traf/
horde/ ibdata1 leechprotect/ mysql.sock sentry_mambo/ test/
root@server:/var/lib/mysql# mv ../mysqlOLD/* ./
mv: overwrite `./host.server.bgsnow.com.err'? y
mv: overwrite `./ibdata1'? n
mv: overwrite `./ib_logfile0'? n
mv: overwrite `./ib_logfile1'? n
mv: overwrite `./mysql-slow.log'? y
root@server:/var/lib/mysql# /etc/init.d/mysql restart
Shutting down MySQL. SUCCESS!
Starting MySQL. SUCCESS!
root@server:/var/lib/mysql# tail -f /var/lib/mysql/host.server.bgsnow.com.err
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 0 43655
091114 13:16:20 InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
091114 13:16:21 InnoDB: Started; log sequence number 0 43655
091114 13:16:21 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist
091114 13:16:21 mysqld ended
Obviously I have forgotten to move back the mysql directory which is responsible for the database for all privileges, databases and so on So moving it back along with the rest of the core files solved the problem:
root@server:/var/lib/mysql# mv ../mysqlOLD/* ./
mv: overwrite `./host.server.bgsnow.com.err'? y
mv: overwrite `./ibdata1'? n
mv: overwrite `./ib_logfile0'? n
mv: overwrite `./ib_logfile1'? n
mv: overwrite `./mysql-slow.log'? y
root@server:/var/lib/mysql# /etc/init.d/mysql restart
Shutting down MySQL. SUCCESS!
Starting MySQL. SUCCESS!
Thus if you have similar problems, the first thing is to check the MySQL error log and don't believe the misleading error about the PID