The victims included a 63-year-old camper who drowned in a storm surge on the German coast and two holidaymakers whose motorboat overturned.
Winds reached 180km/h (112mph) on the Czech Republic's highest mountain.
Some rail services were still suspended in parts of Germany after routes sustained damage.
Disruption was also reported on railways and several roads across the Czech Republic.
Several people were killed by falling trees in strong winds both there and in Poland.
In Germany, a 48-year-old woman and a 56-year-old man died after the boat they were in overturned in the northern state of Mecklenburg-Vorpommern, according to local media. A third person was still missing on Monday.
A freighter - the Glory Amsterdam - ran aground off the German North Sea isle of Langeoog. The authorities are watching for any sign that its 1,800 tonnes of fuel oil might leak.
The ship's crew of 22 are uninjured on board and rescuers are trying to reach them, but massive waves are hampering the effort.
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