The idea behind Econo JIT is to spend less time compiling so that the startup delay is lower for interactive applications. This is actually what you want as soon as you notice that it takes a few seconds to start the application. .NET startup time is already not so slow (also Java :)).
In server-side applications, you want the opposite: you want the perfect code and are ready to wait, because you are probably warming up the application before connecting it to the load balancer. You send an automatic GET to your homepage and other important pages to download and compile.
AFAIK Econo JIT deprecated with .NET 2.0. There is no more choice (with the exception of disabling all optimizations that are a variant of the nuclear bomb).
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