It depends on the company making the software in question. For example, Facebook always uses "du", Microsoft always uses "Sie", Apple and Google use a mixture, depending on product and context. Typically "Sie" is preferred in more formal/business contexts, while "du" is preferred in more informal/social contexts.
To give at least a couple of data points, I've looked through the list of most popular apps of 2015. Of these 10 apps, three (Amazon, Skype, Ebay Kleinanzeigen) use "Sie" and seven (Whatsapp, Facebook Messenger, Facebook, Instagram, Spotify, Shpock, Snapchat) use "du", including the three most popular ones.
Also here are the results for the ten most popular websites (in 2013): Six (Bild, Chip, GMX, eBay, Spiegel, Amazon) use "Sie", and four (Wikipedia, YouTube, Facebook, Google) use "du". Interestingly the four most popular ones use "du".