Those were the criminal proceedings that took that long. The case against Israel right now is the application to institute proceedings. The Rwanda application was filed to the ICJ in 2002 and the final judgment was in 2006. The Yugoslav application was filed to the ICJ in 1993 and final judgment was in 2007.
You're talking about the individual criminal proceedings of the special trial courts (the ICTR and the ICTY) against the perpetrators of charged crimes, which were mandated by the final judgments on the applications to institute proceedings.
The evidence in both of those cases, as far as my memory serves at this moment, included literal mass killings where civilians were lined up and shot, soldiers going door to door killing everyone inside houses, with a heavy helping of torture and mutilations. The stories were very real, as opposed to the allegations in South Africa's application, which is loaded with innuendo, half truths, unverified stories from Qatari and Iranian media, and circular reasoning, a yes a helping of what appear to be very real war crimes. In Rwanda there were plenty of mutilated women and children there to say who did it. If the ICJ institutes proceedings against Israel at a special criminal tribunal, it will take decades to find and prosecute those responsible, and if Israel is telling the truth about what it has for intelligence, most of those proceedings are going to end in aquitals.
Either way, if South Africa's claims were as clear cut and dry as the mob of this community believes they are, the ICJ could have granted any of the preliminary relief South Africa sought, but it didn't. The UN isn't going to open a new tribunal for isolated war crimes of invidiual soldiers as long as Israel is making good faith prosecutions on its own, and it is, as ICJ noted in its preliminary decision, denying South Africa's proposed relief.
Of course, I guess since I've not included links to the the original legal decisions of the ICJ, the moderators might come along and delete this post for being disinformation if they can find an Al Jazeera link that implies in a few second something other than what I've said.