What are the merits of JKS vs PKCS12 for code signing?

When buying a code-signing certificate, what are the merits of starting with a PKCS12 versus JKS certificate? Some vendors give instructions on starting with a JKS or PKCS12 certificate signing request. We'd like to have maximum flexibility in using a purchased cert, especially given the cost. For example, we may be signing more than just Java code (ex: iPhone or Android code signing). What technical considerations should we take into account when choosing either approach?