Are people doing research for Microsoft, Apple, Intel experienced researchers/scientists or just experienced programmers using other people's research? Do they hire full time researchers for their research or do they take experienced/skilled professionals who are familiar working with java, C++ and other commercial technologies?
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).
This is a discipline-specific question. Computer science may have Google, Microsoft, Bell labs -- what do other disciplines have?
I work in survey statistics, and while there are about four or five Ph.D. programs in the world producing survey statisticians and methodologists (Univ of Maryland, Univ of Michigan and Univ of Nebraska, Lincoln in the US; Southampton in UK; Iowa State has a statistics program that is traditionally strong on the survey side; other Ph.Ds come from scattered academic survey statisticians, about another 10 or so people in North America), the papers published in academic journals in the discipline split about evenly between government, industry, and academia-proper. I've heard from friends in chemistry that most of good chemistry research is being done in industry these days, rather than in academia. Don't quote me on this though. National Institutes of Health (US) have a tenure-like system for their researchers, as they are expected to produce top-quality research.