Hi-- I have a pretty standard VPS running Ubuntu 8.1, Apache 2.2, PHP 5 etc. -- standard Lamp stack. I am using suhosin and have tried my best to plug the obvious stuff, since I'm the only user-- there's no SSH access except via pubkey on a non-standard port, there's no root access by SSH, no FTP server running, iptables is set to discard anything outside of basically port 80 or my SSH port (there's no mail server or anything else).

However, I've still been compromised (not badly as far as I can tell) probably by a SQL injection. I've locked down the SQL user (there's only one outside of root, and he's got limited priv, no file etc.)

So I ran nikto to see what I'm doing wrong, and there's a list of things I've never seen, and can't find using "find" or any other method I'm aware of. See below:

+ /autologon.html?10514: Remotely Anywhere 5.10.415 is vulnerable to XSS attacks that can lead to cookie theft or privilege escalation. This is typically found on port 2000.
+ /servlet/webacc?User.html=noexist: Netware web access may reveal full path of the web server. Apply vendor patch or upgrade.
+ OSVDB-35878: /modules.php?name=Members_List&letter='%20OR%20pass%20LIKE%20'a%25'/*: PHP Nuke module allows user names and passwords to be viewed.
+ OSVDB-3092: /sitemap.xml: This gives a nice listing of the site content.
+ OSVDB-12184: /index.php?=PHPB8B5F2A0-3C92-11d3-A3A9-4C7B08C10000: PHP reveals potentially sensitive information via certain HTTP requests which contain specific QUERY strings.
+ OSVDB-12184: /some.php?=PHPE9568F36-D428-11d2-A769-00AA001ACF42: PHP reveals potentially sensitive information via certain HTTP requests which contain specific QUERY strings.
+ OSVDB-12184: /some.php?=PHPE9568F34-D428-11d2-A769-00AA001ACF42: PHP reveals potentially sensitive information via certain HTTP requests which contain specific QUERY strings.
+ OSVDB-12184: /some.php?=PHPE9568F35-D428-11d2-A769-00AA001ACF42: PHP reveals potentially sensitive information via certain HTTP requests which contain specific QUERY strings.
+ OSVDB-3092: /administrator/: This might be interesting...
+ OSVDB-3092: /Agent/: This might be interesting...
+ OSVDB-3092: /includes/: This might be interesting...
+ OSVDB-3092: /logs/: This might be interesting...
+ OSVDB-3092: /tmp/: This might be interesting...
+ ERROR: /servlet/Counter returned an error: error reading HTTP response
+ OSVDB-3268: /icons/: Directory indexing is enabled: /icons
+ OSVDB-3268: /images/: Directory indexing is enabled: /images
+ OSVDB-3299: /forumscalendar.php?calbirthdays=1&action=getday&day=2001-8-15&comma=%22;echo%20'';%20echo%20%60id%20%60;die();echo%22: Vbulletin allows remote command execution. See link
+ OSVDB-3299: /forumzcalendar.php?calbirthdays=1&action=getday&day=2001-8-15&comma=%22;echo%20'';%20echo%20%60id%20%60;die();echo%22: Vbulletin allows remote command execution. See link
+ OSVDB-3299: /htforumcalendar.php?calbirthdays=1&action=getday&day=2001-8-15&comma=%22;echo%20'';%20echo%20%60id%20%60;die();echo%22: Vbulletin allows remote command execution. See link
+ OSVDB-3299: /vbcalendar.php?calbirthdays=1&action=getday&day=2001-8-15&comma=%22;echo%20'';%20echo%20%60id%20%60;die();echo%22: Vbulletin allows remote command execution. See link
+ OSVDB-3299: /vbulletincalendar.php?calbirthdays=1&action=getday&day=2001-8-15&comma=%22;echo%20'';%20echo%20%60id%20%60;die();echo%22: Vbulletin allows remote command execution. See link
+ OSVDB-6659: /kCKAowoWuZkKCUPH7Mr675ILd9hFg1lnyc1tWUuEbkYkFCpCdEnCKkkd9L0bY34tIf9l6t2owkUp9nI5PIDmQzMokDbp71QFTZGxdnZhTUIzxVrQhVgwmPYsMK7g34DURzeiy3nyd4ezX5NtUozTGqMkxDrLheQmx4dDYlRx0vKaX41JX40GEMf21TKWxHAZSUxjgXUnIlKav58GZQ5LNAwSAn13l0w<font%20size=50>DEFACED<!--//--: MyWebServer 1.0.2 is vulnerable to HTML injection. Upgrade to a later version.

I understand about the trace and index, but what about the vbulletin and autologin? I've searched, and I can't find any files like that on the server. I have no idea about the "MyWebServer" stuff, the PHP Nuke, or the Netware/servlet stuff-- there's nothing really on the server except a pretty standard Joomla site (updated to the latest version).

Any help with these messages and/or what I'm doing wrong is very much appreciated.