Apple is now spending roughly a third as much as Microsoft does on research despite generating roughly 50% more revenue. Apple spends roughly one half of what Google spends on research, despite having almost three times the revenue!
Microsoft is a bit of a sleeping giant when it comes to innovation. They do a lot of research and a much of it is of a very fundamental nature that is decades from being commercializable. Of course, they've been doing this for long enough that they currently employ the leading experts in some of the stuff that fit that description ten years ago. Corporate politics under Ballmer (e.g. stack ranking) and a strong aversion to disruptive changes in existing products have really reigned MS's innovation in. It will be interesting to see what happens over the next couple of years as MS software settles into new form-factors for the first time in ages (that goes double if Ballmer is shown the door).
Apple is much more focused than Microsoft on immediately commercializable products. In terms of product-bang for research-buck, Apple probably does a lot better than Microsoft. Still all MS needs to do to rock Apple's tree is shake up it's stodgy corporate structure a bit and become more adventurous.
Google, of course, is a huge innovator, but they do tend to be more like Apple in terms of their focus (i.e. More short term than MS). This focus combined with double the research budget does suggest that Google is the most likely company to out-innovate Apple in the short-term. Indeed, we've started to see this as Android has been gradually getting further ahead of iOS in terms of features even if it has not yet caught up in polish.
Apple is like a solid work-horse running down a race-track. Google is more of a thoroughbred, but got stuck in the gate. Now that Google is threatening for the lead, Apple is applying the whip more generously. MS is like a cheetah laying by the side of the track. It could come out of nowhere and change everything or it could just sit their licking its paws.