Hi,
I certainly second Leo's remark about two weeks being to little time to see all of Germany's railroad. If you're into narrow gauge, Dresden is a good starting point. You may want to check out the Harzer Schmalspurbahn, which runs several narrow gauge lines, one of them leading up the Brocken mountain (1125m). Wikipedia has an article:
http://en.wikipedia.org/wiki/Harzer_Schmalspurbahnen. The HSB is roughly 150 miles northwest of Dresden and would be a good stop on your way north to Molli, which is on the Baltic coast near Rostock. Information in English here
http://www.molli-bahn.de/Englisch.4.0.html.
Tickets: There is a 16-day Interrail-Ticket for one or two zones. Germany forms a zone with Poland, Czech Republic, Switzerland, Austria and some other smaller eastern countries. The one-zone ticket is 286€ and would allow you to check out some of the older railroads in Poland and the Czech Republic which many people here are rather enthused about. For more information, go to
http://www.bahn.de, click "International Guests" in the horizontal navigation bar and then select "Interrail" from the right column.
If you're into freight, there's nothing like the west of Germany, especially the Ruhrgebiet. A former mining region, but still with a lot of steel mills and heavy industry, probably the densest rail network in Europe. I live at the Cologne-Oberhausen main line which averages about 150 freight trains on weekdays. Of course, comparing with American standards, these trains are almost rediculously short and light, but faster and there's many of them. Lots of electrics and diesel here, many privately owned railroad companies, too(Railion, Germany's largest rail freight operator, is still state-owned). However, the interrail ticket for Germany does not cover the Netherlands or France, so you'd have to buy a two-zone ticket if you wanted to check out these countries, too.
For region-specific help, I recommend Germany's largest and most important railroad forum, Drehscheibe Online:
http://www.drehscheibe-online.de. For your questions, select the "Allgemeines" forum. Registration is free, posting in English is no problem.
If you have any further questions, you can also contact me off board.