Microsoft has a prominent research arm, Microsoft Research. Intel has Intel Labs. Both organizations hire research-focused PhDs from both industry and academia, and both employ researchers that have joint appointments on research university faculty. Employees at both organizations also routinely publish fundamental research at peer-reviewed conferences and workshops, and in journals.
Apple is a tougher nut to crack -- they spend truckloads of money on R&D, but rarely publish in peer-reviewed venues. However, they do hire plenty of PhDs, who do focused research on products that sometimes turn into the next iPhone.
All three companies file many patents, as well.
Many other big companies also have research labs, and openly hire researches specifically working on fundamental research. However, as with any company, research tends to be focused in the direction that could eventually produce profitable products -- if you are considering a research job at a company, you should take this into consideration. For what it's worth, Microsoft Research seems to be closer to the "research for the sake of science" than some other labs, although there are others (notably, labs such as (formerly) Xerox PARC and Bell Labs are famous for groundbreaking fundamental research).