FYI, I'm getting the same problem on a OS X 10.8.2 box at a customer site. 
ScriptAlias is set to /apps/WebObjects in webobjects.conf (I always rename 
apache.conf to webobjects.conf) but I get:

  [Mon Mar 25 16:35:30 2013] [error] [client 207.253.87.97] File does not 
exist: /Library/Server/Web/Data/Sites/Default/app

And I do known that webobjects.conf is read because if I try to load the 
modules two times, Apache will throw a warning.

> It sounds like it is trying to use the CGI adaptor.  Does your httpd.conf 
> file include this line?
> 
> Include /System/Library/WebObjects/Adaptors/Apache2.2/apache.conf
> 
> Is the path correct?
> 
> What does this output
> 
> sudo apachectl configtest
> 
> 
> Chuck
> 
> 
> On 2013-03-18, at 11:40 AM, Baiss Eric Magnusson wrote:
> 
>> 
>>> Check this line in /etc/apache2/httpd.conf:
>>>  ScriptAliasMatch ^/cgi-bin/((?!(?i:webobjects)).*$) 
>>> "/Library/WebServer/CGI-Executables/$1"
>>> 
>>> Make sure that it matches exactly.
>>> Chuck
>>> 
>> It matches.
>> 
>>> Pascal writes:
>>> Check for errors in /var/log/apache2/error_log
>> 
>> Ah, all 3 "JavaMonitor Name link clicks" generate the same msg in log file, 
>> regardless of application selected.
>> 
>>> [Sat Mar 16 2013] [error] [client 173.160.202.me]
>> 
>>> File does not exist: /Library/WebServer/Documents/cwd/cgi-bin,
>> 
>>> referer: 
>>> http://173.160.202.xxx:56789/cgi-bin/WebObjects/JavaMonitor.woa/wo/YxUK1TOAKPj8IqGMBCjX00/4.0.1.0
>> 
>> ****************
>> And I noticed what a call from the home page of track-your-finances.com to 
>> the tyf WO application from somewhere afar generated:
>> 
>>> [client 123.151.148.200] File does not exist: 
>>> /Library/WebServer/Documents/tyf/cgi-bin, referer: 
>>> http://track-your-finances.com
>> 
>> Is this enough information for someone to suggest the "next step"?
>> Prev note: the applications are running according to process monitor.
>> 
>> ...
>> Baiss Eric Magnusson
>> cascadewebdesign.com
>> 
>> 
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> 
> -- 
> Chuck Hill             
> Executive Managing Partner, VP Development and Technical Services
> 
> Practical WebObjects - for developers who want to increase their overall 
> knowledge of WebObjects or who are trying to solve specific problems.    
> http://www.global-village.net/gvc/practical_webobjects
> 
> Global Village Consulting ranks 13th in 2012 in BIV's Top 100 Fastest Growing 
> Companies in B.C! 
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