I believe the general recommendation for new applications is to use NETCONF because it is standardized. The RPC API is identical between the two languages, but there are some configuration related tasks that Junoscript can do which NETCONF cannot (at least not yet, AFAIK) like retrieve the configuration in text format, or compare the candidate config to a different configuration.
I've written a few op scripts with SLAX, and am now looking to use Perl to write scripts to interact with Juniper routers. I see that there are noth NETCONF and JUNOScript APIs for Perl available and I'm trying to decide on which one to use. The NETCONF seems attractive becasue it is RFC based and appears more generalized, while JUNOSCript is obviously Juniper specific. Other than that I wanted to see if anyone knew of any compelling reasons to choose one over the other.