There are some teams that would have been different than in OTL:
Germany: Without being the host, the German team would have had to qualify. In OTL, Klinsmann/Löw had a lot of time to experiment with the squad and tactics, thereby testing a wide range of players. Later came a "wake-up call" in their 1-4 defeat to Italy shortly before the tournament. In a qualification round, there would have been other priorities (mainly, a solid qualification after the embarrassing exit at Euro 2004) and therefore possibly a more 'conservative' approach to the squad. This also means that another European team might not have made the tournament (possibly Switzerland).
England: The English team had real difficulties with the hot German summer back in 2006. Remember Becks throwing up during the game against Ecuador? The South African winter climate probably suited them better. And in 2006, the Terry-Gerrard-Lampard-Beckham-Rooney axis worked way better than four years later. With an easy preliminary group, they might make the semi-finals or even the final in South Africa '06.
Cote d'Ivoire were probably at their best phase in 2006, but had a tough group stage. Maybe they'd have had a better run on the home continent.
As for the European semi-final, I think that would still be the case. Portugal, Italy and France had very good teams. The other candidates would be Germany, England and the Netherlands. Brazil would still have Carlos Alberto Pareira as coach, who sort of had a laissez-faire "give Kaka, Ronaldinho and Adriano the ball and watch the sparks fly"-approach to tactics, which didn't work against teams such as Italy or France.