Honestly, I haven't found any one online agency that's consistently cheaper than the others for Europe. I've been using the meta search engines like kayak and hotelscombined to sift for deals. I'm also keeping an eye open for the code discounts.

I have in the past occasionally found good deals on HRS and, for this trip, I did pick up a 3-star hotel near Freiburg, Germany that was about 35% less on HRS than anyone else. It's unpredictable, though, so you just have to search.

I have noticed that booking.com has a lot of "b&b" type places, which makes searching for these easier than combing the tripadvisor reviews and trying to contact the properties directly. That is still a good strategy to include, but it's time consuming, and it's hard to search for more than one town on tripadvisor.