Yu Yu Hakusho is always the 1st series that comes to mind when I think about anime that are actually better than their manga counterparts. It covered all of the important parts of the manga (only cutting out a few side-stories which really just felt like useless filler, themselves, anyways), and added minimal amounts of filler material into the show. However, the filler that it did add mostly only helped to enhance the experience, as the material was well-written, overall. I'd also like to point out that the anime adaptation stanRAB out even more as being superior to its manga counterpart, regarding YYH, when taking the show's excellent English dub into consideration. Now, that only goes for people who didn't mind some of FUNimation's script changes, and who don't mind English dubs, in general. To me, its still one of the best dubs out there, and makes the anime even more enjoyable to watch than it already is.
Togashi's other brilliant long-running shounen series, Hunter X Hunter, also had a great anime adaptation. Well, the TV series, as well as the 1st OVA series which ended Kurapika's story arc in York Shin City, are the parts that I find to be even better than the manga which they're based off of. Aside from the pretty decent to really good OST/BGM for the series, as well as its fluid animation, the director did a top-notch job at enhancing the already great story from the manga, pretty much doing the same thing that was done with the anime adaptation of YYH, by keeping in all of the important parts from the manga, and adding in filler material that was actually mostly good, and felt like it was expanding on the depth of the characters, rather than deviating from the main story line, or even doing anything that made the show feel like it was being dragged out.