The main difference is that Open Source programs can handle DNG since the specs are open (although mainly developed by Adobe). For CR2 (proprietary format of Canon) it always needs reverse engineering of Canon's import algorithms which can result in slight differences - or it needs the manufacturer software. Canon's DPP comes free, Nikon's software is only a trial version (AFAIK).
Regarding processing speed there is no difference.
As we can see with various other file formats (XML text documents, PNG image files) Open Source is the way to go into the future if one doesn't want to get stuck (or bound) to royalties, software licenses and proprietary software.