A maioria dos diretórios deve ser 755 e de propriedade do root. Infelizmente nem tudo deve ser isso. Se você fizer uma alteração de permissão recursiva, causará muito mais dano. Na minha máquina, eu tenho:
mojo-jojo david% sudo find /var -type d ! -perm 755 -ls 278532 4 drwxrwsr-x 2 root staff 4096 Oct 20 2008 /var/local 286930 4 drwx-wx--T 2 root crontab 4096 Sep 9 2008 /var/spool/cron/crontabs 286848 4 drwxrwx--T 2 daemon daemon 4096 Jul 10 2008 /var/spool/cron/atspool 286849 4 drwxrwx--T 2 daemon daemon 4096 Oct 21 2008 /var/spool/cron/atjobs 319499 4 drwx--x--- 3 root lp 4096 Oct 21 2008 /var/spool/cups 319500 4 drwxrwx--T 2 root lp 4096 Oct 20 2008 /var/spool/cups/tmp 352575 4 drwxr-x--- 5 Debian-exim Debian-exim 4096 Mar 28 09:03 /var/spool/exim4 352624 4 drwxr-x--- 2 Debian-exim Debian-exim 4096 Aug 5 07:02 /var/spool/exim4/msglog 352622 4 drwxr-x--- 2 Debian-exim Debian-exim 4096 Dec 14 2008 /var/spool/exim4/db 352623 4 drwxr-x--- 2 Debian-exim Debian-exim 4096 Aug 5 07:02 /var/spool/exim4/input 279126 4 drwxrwsr-x 2 libuuid libuuid 4096 Oct 21 2008 /var/lib/libuuid 352603 4 drwxrwx--- 2 logcheck logcheck 4096 Oct 22 2008 /var/lib/logcheck 320214 4 drwxrwx--- 2 root polkituser 4096 Oct 21 2008 /var/lib/PolicyKit 352614 4 drwxrwxr-x 2 munin munin 4096 May 3 09:05 /var/lib/munin/plugin-state 270524 4 drwx------ 10 postgres postgres 4096 Jul 29 04:07 /var/lib/postgresql/8.3/main 270533 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_twophase 270540 4 drwx------ 7 postgres postgres 4096 Dec 13 2008 /var/lib/postgresql/8.3/main/base 1106278 4 drwx------ 2 postgres postgres 4096 Dec 18 2008 /var/lib/postgresql/8.3/main/base/pgsql_tmp 311894 4 drwx------ 2 postgres postgres 4096 Jul 29 04:07 /var/lib/postgresql/8.3/main/base/11511 270542 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/base/1 270937 4 drwx------ 2 postgres postgres 4096 Mar 28 09:29 /var/lib/postgresql/8.3/main/base/16385 311320 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/base/11510 270543 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_tblspc 270527 4 drwx------ 2 postgres postgres 4096 Aug 5 08:32 /var/lib/postgresql/8.3/main/global 270528 4 drwx------ 3 postgres postgres 4096 Dec 17 2008 /var/lib/postgresql/8.3/main/pg_xlog 270529 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_xlog/archive_status 270535 4 drwx------ 4 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_multixact 270538 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_multixact/offsets 270536 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_multixact/members 270532 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_subtrans 270530 4 drwx------ 2 postgres postgres 4096 Dec 12 2008 /var/lib/postgresql/8.3/main/pg_clog 321312 4 drwxrwx--T 3 root gdm 4096 Jul 29 08:17 /var/lib/gdm 1729012 4 drwx------ 2 mysql mysql 4096 Feb 3 2009 /var/lib/mysql/newforms_sess 1728971 4 drwx------ 2 mysql mysql 4096 Feb 16 21:38 /var/lib/mysql/newforms 369895 4 drwxrwxr-x 3 root tomcat6 4096 Dec 17 2008 /var/lib/tomcat6/webapps 270506 4 drwxr-x--- 15 root root 4096 Apr 25 11:50 /var/lib/puppet/clientbucket 271123 4 drwxrwx--- 3 root root 4096 Apr 18 13:51 /var/lib/puppet/clientbucket/* 270483 4 drwxrwx--x 6 root root 4096 Mar 28 19:21 /var/lib/puppet/ssl 270490 4 drwxr-x--- 2 root root 4096 Mar 28 19:21 /var/lib/puppet/ssl/private_keys 270488 4 drwxr-x--- 2 root root 4096 Mar 28 19:21 /var/lib/puppet/ssl/private 270481 4 drwxr-xr-t 2 root root 4096 Aug 5 08:18 /var/lib/puppet/state 534313 0 drwx------ 3 root Domain Users 60 Jul 29 21:30 /var/run/sudo 534314 0 drwx------ 2 root Domain Users 100 Aug 5 08:32 /var/run/sudo/david 9242 0 dr-x--x--x 2 lp lpadmin 40 Aug 5 07:43 /var/run/cups/certs 8006 0 drwxrwxrwt 2 puppet puppet 60 Aug 2 07:43 /var/run/puppet 7877 0 drwxr-x--- 2 root winbindd_priv 60 Aug 2 08:26 /var/run/samba/winbindd_privileged 7463 0 drwxr-x--- 2 Debian-exim Debian-exim 60 Jul 29 04:07 /var/run/exim4 6880 0 drwxrwsr-x 2 postgres postgres 100 Jul 29 04:07 /var/run/postgresql 6172 0 drwxrwx--- 2 root polkituser 40 Jul 29 04:07 /var/run/PolicyKit 6016 0 drwxrwxr-x 2 root utmp 40 Jul 29 04:07 /var/run/screen 278583 4 drwxrwsr-x 2 root mail 4096 Oct 21 2008 /var/mail 327995 4 drwxrwxrwt 2 root root 4096 Apr 9 07:35 /var/crash 278535 4 drwxrwxrwt 2 root root 4096 Aug 2 10:34 /var/tmp 2878 0 drwxrwxrwt 4 root root 100 Aug 5 07:43 /var/lock 320430 4 drwxrwxr-x 4 root lp 4096 Mar 28 09:12 /var/cache/cups 320432 4 drwxrwxr-x 2 root lp 4096 Oct 20 2008 /var/cache/cups/rss 278548 4 drwx------ 2 root root 4096 Aug 5 08:30 /var/cache/ldconfig 271257 4 drwx------ 2 tomcat55 adm 4096 Nov 18 2008 /var/cache/tomcat5.5 287018 4 drwxr-sr-x 44 man root 4096 Aug 5 07:43 /var/cache/man 287178 4 drwxr-sr-x 2 man root 4096 Aug 5 07:43 /var/cache/man/* 541847 4 drwxr-x--- 3 tomcat6 adm 4096 Jun 20 18:43 /var/cache/tomcat6 327693 4 drwxrwsr-t 2 root admin 4096 Oct 21 2008 /var/cache/jockey 352620 4 drwxr-s--- 2 Debian-exim adm 4096 Aug 5 07:43 /var/log/exim4 328117 4 drwxr-x--- 3 root adm 4096 Aug 2 07:43 /var/log/samba 353025 4 drwx------ 3 root root 4096 Oct 22 2008 /var/log/samba/cores 353026 4 drwx------ 2 root root 4096 Oct 22 2008 /var/log/samba/cores/winbindd 279487 4 drwxr-sr-x 2 news news 4096 Oct 21 2008 /var/log/news 352612 4 drwxr-x--- 2 munin adm 4096 Aug 5 07:43 /var/log/munin 311823 4 drwxrwxr-t 2 root postgres 4096 Aug 2 07:43 /var/log/postgresql 288323 4 drwxr-x--- 2 tomcat55 adm 4096 Aug 4 07:52 /var/log/tomcat5.5 328912 4 drwxr-x--- 2 root adm 4096 Aug 2 07:43 /var/log/apache2 328064 4 drwxr-s--- 2 mysql adm 4096 Jan 29 2009 /var/log/mysql 369892 4 drwxr-x--- 2 tomcat6 adm 4096 Aug 4 07:52 /var/log/tomcat6 294961 4 drwxr-x--- 2 puppet puppet 4096 Aug 2 07:43 /var/log/puppet
Haverá muitos mais arquivos com permissões diferentes. Espero que isso te dê uma ideia do que consertar.