Captain... what Celtic says is very true... if you don't hold an EU passport and you are not planning to fly there then don't bother with a JAA license. A South African license is acceptable everywhere else.
The standards of training in SA are very good and that is recognised in other parts of the world... look how may SA pilots are flying for Cathay Pacific, Singapore, Air Mauritius etc.
Not sure exactly what the latest JAA news is but the conversion requirements depend on your (foreign) qualifications and experience... once you have a few years with an airline it should be no problem to convert.
43 Air School is the best place to go in South Africa. An great learning environment and very professional. Not necessarily the cheapest but you will walk out of there within a year (if you work hard !) with everything you need.
Good luck in whatever you decide.
Cheers Dutchie