Hi Manish,
Can I ask which versions of Scala and ScalaTest are you using?
If you're using a 2.0 milestone or snap release, you can annotate your classes with @UnitTests or @IntegrationTests (if you create those tag annotations). That will then cause the tests inside those classes to be tagged as such, allowing you to include/exclude such tests. But both categories of test class will be discovered and show up in your report, so that's probably not what you want.
Another approach which will also work in 1.8 or later is to use a naming convention for your test classes. Instead of ending your test classes with "Spec", end them with either "UnitSpec" or "IntegSpec". Or USpec and ISpec, etc., if you prefer something more concise. So you might have names like WidgetUSpec and WhatsitISpec, etc.
You can then tell Runner to discard and not inspect any class name that doesn't end in "ISpec" in one target of your build, and in "USpec" in another target. For the details, check out the Suffixes to discover section here: