A very interesting research paper titled "Apache Prefork MPM Vulnerabilities" was released a few days ago, as you can see in the corresponding Bugtraq post. The paper describes, in detail, the dangers of allowing third-parties to run code under the same account as the Apache web server. This normally happens when dynamic content is produced using Apache modules (e.g. PHP) or when CGI scripts are configured to run without suEXEC. This topic itself is not new. You will find several articles on runtime process infection following this Google search link. I warn about this problem throughout my book and especially in Chapter 6, which is dedicated to those situations when more than one party is using the one Apache installation. However, it is one thing to know that something is possible and another to demonstrate, step by step, how it is done. Another interesting finding resulting from this paper is that it is possible to send a SIGUSR1 signal, as root, to any process on the system instead of just to Apache children processes. This is an issue that will have to be fixed in one of the future versions of Apache.
This problem with running code as the same identity as the web server is well understood (and has been for years) among the advanced Apache users. The solution is to always execute CGI scripts through suEXEC and to never allow third parties access to any of the modules. The real problem is that, as with any other product, there are few people who understand Apache inside out (and they can protect themselves) but there also those who are using the technology but do not have the luxury of learning everything there is about it (and there are many legitimate reasons for that).
The solution is obvious. Apache must be safe out of the box! We should dispense with the idea of running things in the same process. Process isolation facilities (either suEXEC or something else) should be installed and running by default on all installations. We can and should make provisions for those who know what they are doing to shoot themselves in the foot, of course. But the only reason to attempt to run things in the same process is performance and I suspect, in this day and age, virtually all users will be happy with the performance of their web server doing things in a secure manner.