There are no Apple Stores in Germany, but there is a chain called Gravis that has sold Apple gear for years. Now the Gravis shops will also carry the iPhone 3G and will sell them with T-Mobile contracts according to Heise (German).

Apple is supposedly opening an Apple store in Munich in 2008. The building is still a construction site in early stages. Apple is already hiring personal for the Munich Apple store though.
In any case the iPhone 3G will not only be available in T-Mobile shops but also at Gravis - maybe a good thing to know if there are lines at the T-Mobile shop on iPhone 3G launch day (11th of July).

On the other hand the T-Mobile online shop is taking pre-orders for the iPhone 3G already.