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Gracias por la sugerencia. Eliminé la configuración de apache.conf y solo dejé la del httpd.conf, y se arregló el primer error. El segundo no lo he arreglado pero no creo que sea un problema con eso pero aun me sale el error 403. Al realizar el ls -l /var/www/cgi-bin me da los siguientes parámetros...

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-rwxr-xr-x 1 l0rd5had0w root 76 2008-08-09 21:25 Prueba1.pl
-rw-r--r-- 1 l0rd5had0w root  0 2008-08-09 21:24 Prueba1.pl~

Ya probé nuevamente a darle el permiso 755 pero me muestra el mismo mensaje de error... gracias por su ayuda.

Salu2 y gracias por todo...

Bueno, a la carpeta supuestamente le di permisos con sudo chown usuario cgi-bin. Según leí de esa forma se hacía. Me podría decir por favor dónde está el error.log, en qué ubicación. Así lo leo y posiblemente de esa manera solucione el problema. Gracias por su ayuda...

Pues no sé cómo cambiar esos valores, me imagino que si los realizo con chmod 755 sí funciona porque ese sí da permisos de lectura, escritura y ejecución...

Le dejo una copia de mi error.log para ver si usted descubre el problema con ello porque yo no logro identificarlo...

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[Sat Aug 09 09:05:38 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 10:36:55 2008] [notice] caught SIGTERM, shutting down
[Sat Aug 09 11:19:42 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 11:36:33 2008] [error] [client 127.0.0.1] File does not exist: /var/www/prueba.cgi
[Sat Aug 09 11:45:55 2008] [notice] caught SIGWINCH, shutting down gracefully
[Sat Aug 09 11:47:15 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 12:24:46 2008] [error] [client 127.0.0.1] File does not exist: /var/www/cgi-bin
[Sat Aug 09 12:24:53 2008] [error] [client 127.0.0.1] (13)Permission denied: exec of '/usr/lib/cgi-bin/prueba.cgi' failed
[Sat Aug 09 12:24:53 2008] [error] [client 127.0.0.1] Premature end of script headers: prueba.cgi
[Sat Aug 09 12:28:04 2008] [error] [client 127.0.0.1] (13)Permission denied: exec of '/usr/lib/cgi-bin/prueba.cgi' failed, referer: http://perlenespanol.com/foro/viewtopic.php?t=742.html
[Sat Aug 09 12:28:04 2008] [error] [client 127.0.0.1] Premature end of script headers: prueba.cgi, referer: http://perlenespanol.com/foro/viewtopic.php?t=742.html
[Sat Aug 09 12:33:16 2008] [error] [client 127.0.0.1] (13)Permission denied: exec of '/usr/lib/cgi-bin/prueba.cgi' failed
[Sat Aug 09 12:33:16 2008] [error] [client 127.0.0.1] Premature end of script headers: prueba.cgi
[Sat Aug 09 12:37:39 2008] [notice] caught SIGWINCH, shutting down gracefully
[Sat Aug 09 13:39:01 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 19:21:07 2008] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico
[Sat Aug 09 20:11:40 2008] [error] [client 127.0.0.1] File does not exist: /var/www/cgi-bin
[Sat Aug 09 20:11:51 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /usr/lib/cgi-bin/
[Sat Aug 09 20:12:41 2008] [error] [client 127.0.0.1] script '/var/www/Prueba1.php' not found or unable to stat
[Sat Aug 09 21:38:16 2008] [error] [client 127.0.0.1] Options ExecCGI is off in this directory: /var/www/Prueba1.pl
[Sat Aug 09 21:47:13 2008] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico
[Sat Aug 09 22:01:55 2008] [error] [client 127.0.0.1] Options ExecCGI is off in this directory: /var/www/Cgi-Bin/Prueba1.pl, referer: http://localhost/Cgi-Bin/
[Sat Aug 09 22:02:13 2008] [error] [client 127.0.0.1] Options ExecCGI is off in this directory: /var/www/Cgi-Bin/Prueba1.pl, referer: http://localhost/Cgi-Bin/
[Sat Aug 09 22:05:31 2008] [error] [client 127.0.0.1] Options ExecCGI is off in this directory: /var/www/Cgi-Bin/Prueba1.pl, referer: http://localhost/Cgi-Bin/
[Sat Aug 09 22:47:23 2008] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico
[Sat Aug 09 23:04:24 2008] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico
[Sat Aug 09 23:13:46 2008] [error] [client 127.0.0.1] script not found or unable to stat: /usr/lib/cgi-bin/Prueba1.pl
[Sat Aug 09 23:13:55 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /usr/lib/cgi-bin/
[Sat Aug 09 23:15:14 2008] [error] [client 127.0.0.1] File does not exist: /var/www/\xc3\xa7
[Sat Aug 09 23:15:23 2008] [error] [client 127.0.0.1] File does not exist: /var/www/Cgi-Bin
[Sat Aug 09 23:15:46 2008] [notice] Graceful restart requested, doing restart
[Sat Aug 09 23:15:47 2008] [warn] The ScriptAlias directive in /etc/apache2/apache2.conf at line 301 will probably never match because it overlaps an earlier ScriptAlias.
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
[Sat Aug 09 23:15:48 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 23:15:57 2008] [notice] Graceful restart requested, doing restart
[Sat Aug 09 23:15:57 2008] [warn] The ScriptAlias directive in /etc/apache2/apache2.conf at line 301 will probably never match because it overlaps an earlier ScriptAlias.
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
[Sat Aug 09 23:15:57 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 23:18:24 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
[Sat Aug 09 23:23:50 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
[Sat Aug 09 23:34:05 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
[Sat Aug 09 23:49:08 2008] [notice] Graceful restart requested, doing restart
[Sat Aug 09 23:49:09 2008] [warn] The ScriptAlias directive in /etc/apache2/apache2.conf at line 301 will probably never match because it overlaps an earlier ScriptAlias.
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
[Sat Aug 09 23:49:09 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 23:50:00 2008] [notice] Graceful restart requested, doing restart
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
[Sat Aug 09 23:50:00 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 23:52:12 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /usr/lib/cgi-bin/
[Sat Aug 09 23:56:11 2008] [notice] Graceful restart requested, doing restart
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
[Sat Aug 09 23:56:12 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sat Aug 09 23:58:44 2008] [notice] Graceful restart requested, doing restart
apache2: Could not reliably determine the server's fully qualified domain name, using 127.0.1.1 for ServerName
[Sat Aug 09 23:58:44 2008] [notice] Apache/2.2.8 (Ubuntu) PHP/5.2.4-2ubuntu5.3 with Suhosin-Patch configured -- resuming normal operations
[Sun Aug 10 00:00:48 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
[Sun Aug 10 00:06:10 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
[Sun Aug 10 00:17:49 2008] [error] [client 127.0.0.1] File does not exist: /var/www/favicon.ico
[Sun Aug 10 00:17:54 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/
[Sun Aug 10 00:39:20 2008] [error] [client 127.0.0.1] attempt to invoke directory as script: /var/www/cgi-bin/

Todo eso fue los errores desde la configuración hasta ahora. Tal vez de esta forma usted identifique qué causa el problema que tengo. Ante todo, gracias por su ayuda, y yo por el momento me voy a dormir mañana a seguir batallando para arreglar esto gracias...

Ahhh, se me olvidaba. Al realizar el ls -al /var/www/cgi-bin me aparece lo siguiente. Creo que sí es un problema con permisos...

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drwxr-xr-x 2 l0rd5had0w root 4096 2008-08-09 21:25 .
drwxr-xr-x 7 l0rd5had0w root 4096 2008-08-09 23:01 ..
-rwxr-xr-x 1 l0rd5had0w root   76 2008-08-09 21:25 Prueba1.pl
-rw-r--r-- 1 l0rd5had0w root    0 2008-08-09 21:24 Prueba1.pl~

Salu2 y hasta la próxima, o sea, mañana, jeje XD Gracias por su ayuda, fue de mucha utilidad...

Hola Salu2, pues chown() ya se los agregué a la carpeta y al fichero pero aun así no hay forma. Lo que no entiendo es que cuando lo tengo como cgi-bin me aparece ese error de permiso; cuando lo cambio a Cgi-Bin no me aparece el error de permisos en la carpeta pero si en el fichero... será que el problema se puede deber a que en el sistema existe la carpeta /usr/lib/cgi-bin y yo creé la /var/www/cgi-bin, bueno, qué otro posible problema se podría estar presentando? Ya leí el how-to de Apache y lo seguí paso a paso. No sé qué otra cosa podría ser... Espero ayuda gracias...