John C Dvorak just posted an interesting opinion piece on Microsoft's bid to acquire Yahoo!. I like his rationale here. Did you invest in a company (Y!) for what the company has to offer and its potential future or did you invest, waiting for Microsoft to buy it? For most, it is (or should be) the former. By going with the Microsoft buyout, you're giving up on your investment. Further I would add, sure you get Microsoft stock (which you can get anyways without the buyout), but you really have no idea what's in store for the future merged company. What parts of Y! stay and which parts go?
Oh, and if you've ever been one of these acquired companies, how often has the "new plan" panned out? Typically the highly skilled employees from the acquired company leave for new jobs; the acquiring company never lets the newly acquired company influence and teach the valuable parts they bring to the table; and so you are left with a bunch of assets now being ran by inexperienced folks stuck in an old business model. (You could say I carry some baggage.)
So if you're an investor in Y!, we don't need one less company in this space; we need a company that's allowed to try new things in a new space and continue to give the Google and Microsoft giants some competition once in a while.