Ive seen all kinds of various colors and patterns, so you really have a lot of lattitude. However, I would definitely use earth tones (more grayish) since the weather (cold and rain) tend to wear on them. I have seen some reddish brick colored cobblestones on occassion as well.
If I had to categorize them, I would say the cobblestone used on pedestrian or side streets are mainly square-like in shape about 1-2 inches in length and width with slightly rounded edges. I've seen flat top and slightly roudned tops. I have also seen on occasion some longer ones mostly used in large open areas such as the central market areas. Its hard to say because there are so many variances. As far as cracks I'd recommend either an earthy dirt or dark black. Again, it varies.
I've lived for 3 years in Germany about 30 min from Regensburg and been all over. If you'd like I can try to get some pics, but right now my work hours don't allow much leeway. I can snap and post some in about 2 weeks if that is cool.