It depends :-)
On...
- ...where and how you want to deploy the application
- ...the skillsets of the engineers in your organization
- ...what third-party components you want to integrate with or incorporate
Deployment
If you need to be able to deploy the solution on any of dozens of different possible platforms, you may find that you're better off with PHP than Java (for example). There are hundreds of thousands of Java hosting providers out there, but there are probably millions of PHP hosting providers. (And I say this as a Java-head who dislikes PHP.)
This goes to OS as well. Mono aside, .Net stuff is going to limit you to Windows-based deployment (or lagging behind the cutting edge and having to very, very rigorously test each and every 3rd party component you bring in, to ensure that it doesn't have Mono...issues).
Skillsets
Coming up to speed in an environment or language is non-trivial. For most of us, picking up the basics is pretty quick, but you may not be making the best architectural/design decisions because you're (comparatively) weak on the environment/language. Skillsets count.
Related to this: Skillset hiring counts. Is it easier (and/or cheaper) to hire PHP devs with 3-4 years of experience, or Java devs with 3-4 years of experience, or C# devs, or...?
Buying/finding/integrating vs. building
In your target area of development, which server-side components or packages will you want to integrate with? PHP has a vast array of things available for it, as does Java, as does C# or ASP.Net. But they're different things (by and large), so you'll want to look at what you actually want to use.
Conclusion
So I think it's less a matter of compiled vs. scripted (in today's world), and more a matter of what's the best fit by other criteria for what you're trying to do.
Addendum: Both/And
And of course, there's always "both/and". For instance, I do work in two main, unrelated environments right now, both using a combination of scripted and compiled resources. (One of them is Java + JavaScript via Rhino on Tomcat, the other is compiled COM objects + JScript [again, server-side] on IIS.)