You can take a look at the onsen ranking to judge which one is the best(overall ranking as of 2007, 1. Kusatsu 2. Yufuin 3. Kurokawa 4. Noboribetsu 5. Ibusuki ) but I will give you my personal ranking here:)
My favorite onses are: (I couldn't narrow it down to one...)
I think onsen is similar to wine. Everyone has different tastes. I prefer to drink the white wine now but I used to like to drink the full-bodied red wines. Before that I preferred the whine ones. So, my taste changed from white - red - white. When I started to go onsening, I first liked the transparent water without any smell. Then, I became a big fan of the milky water type with a heavy sulfur smell. Still, I cannot help smiling when I soak myself in the milky sulfur onsen, but I think I started to appreciate the transparent sufur ones. Maybe I am just getting old.... Anyway, the ones listed above are mainly milky sulfur type. Hope you enjoy them.