Looking at pkgsrc/lang/sun-jre13 as well as its CVS history it looks  
like that package has been modified to recognize in the case of  
Darwin the JRE version supplied by the OS.
At least as of today, there are some issues involved though:
a) the current version of Mac OS X, 10.4, comes with JRE 1.4, not 1.3
b) more severely, the package does not (no longer?) work on Darwin  
since it tries to install patches where there has been nothing to  
patch in the working directory

I think the best solution would be to remove the Darwin-specific  
stuff from the package and make it *-*-i386 only again.
However, one would need another mechanism to tell pkgsrc (on systems  
like Darwin and maybe also Solaris) to use the system-supplied JRE  
which is version X.Y (for cases where that  might matter). Is there  
already such a mechanism? In the end the package for Darwin at least  
tries to do exactly that. I'd prefer however a mechanism which does  
not even make pkgsrc descend into that package on systems where it  
should used the OS-supplied version of JRE.
The same issue seems to exist for sun-jdk13, BTW.

-- 
Georg Schwarz    http://home.pages.de/~schwarz/
georg.schwarz@freenet.de  +49 178 8545053