Figure 1: Representative acquisitions of Yahoo, Google, and Microsoft (from this blog)
A Microsoft takeover of all or some of Yahoo will be a good thing for Microsoft in it's battle to unseat Google from the Internet's helm. Perhaps a later Microsoft-Facebook arrangement will finally present a credible challenge to Google. I doubt if the Yahoo board will now agree to anything less than the 72% premium over the original share price Microsoft had offered earlier, so Yahoo shareholders will also come out wealthier from the deal. End users are likely to benefit from a stronger alternative to Google as well.
But one quarter will suffer quietly in the short to medium term: startup companies. Yahoo and Microsoft are some of the most prolific startup acquirers (see Figure 1, from this blog). Yahoo merging with Microsoft removes a big buyer for many startup companies. Moreover, Microsoft will have that much less cash (approximately $44B less based on the first MS offer) to throw at startup acquisitions. With the credit supply tightening up and the economy slowing down, you can be sure of a capital drought ahead for many Internet and software startups.