I guess Web Applications is like Stack Overflow, but for web applications. Why is there Server Fault and Pro Webmasters? Is http://webmasters.stackexchange.com/ somewhere between http://serverfault.com/ and http://webapps.stackexchange.com/?
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Troubleshooting server related stuff is just a small subset of the on topic scope at Webmasters. Webmasters is for questions related to the day to day task of maintaining a web site, and everything that doing so entails. So yes, a question regarding some kind of web server configuration is on topic there. A common question would be something
If you're building out your own server farm and have lots of questions about how to plan the infrastructure and connect all of those moving pieces together, your question should go to Server Fault. If you're having trouble getting OSQA working on DreamHost, it's probably:
There's also a bit of overlap with the UNIX/Linux sites, since naturally webmasters will also have questions regarding how to do certain things. It just comes down to "What site focuses the most on the core of the problem I'm having?" If the core of the problem is about running and maintaining a web site, ask it on Webmasters. If you just can't get Apache working, try Server Fault. If you want to know how to do something via shell on your VPS, perhaps try the Unix/Linux / Ubuntu sites.
While the same question might be technically on topic for all four, it comes down to asking it on the site that you think best fits the problem.