Hakone is one of the best places I have been to in Japan as far as hot springs go. After travelling all day, hiking up Owakudani, and having sulphur smell stuck in your nose, going back to Hakone village at night to dip in an onsen is the perfect end to the day.
There are a variety of hot springs to choose from, but the one we went to (http://www.hakoneyuryo.jp/english/hotsprings/) had several terraced pools with a very natural/traditional setting under a canopy of trees.
The village of Hakone itself compliments the hot springs well as the whole town is built on the side of a mountain with a stream running down the middle. All in all it makes for a very peaceful and relaxing end to the day. Highly recommend!