How will the US Airways and American Airlines merger affect frequent flyer miles?

If past merger information is any indication of what will happen you can take a look at recent mergers of United and Continental.

The accounts of frequent flyers have been merged into one without the loss of miles. So until the announcement from AA and USAir come out you could operate under the assumption that your miles will remain intact.

At the moment you cannot earn miles on US Airways in your American Airlines AAdvantage account:

At this time, American and US Airways will remain separate companies and each company will maintain its current loyalty program.

No-one knows for sure what will ultimately happen with the programs - possibly even American and US Airways at this stage - although it seems fairly sure from their official publicity that there will be a merged frequent flyer account. The publicity also states that it's likely to be with Oneworld, so I wouldn't be surprised if US Airways' Dividend Miles program is merged into American's AAdvantage, presumably gaining earning/spending miles privileges on Oneworld, and losing similar status with Star Alliance. (Related Economist article)

If you know for sure you will fly US Airways soon, and it's a non-trivial number of miles you'll earn, it might be worth you signing up for the US Airways program now, earning the miles, and hoping they give you the opportunity to merge them into your AAdvantage account later. I certainly wouldn't worry that your US Airways miles will suddenly become worthless - that would be a huge PR misstep, and possibly have legal and accounting issues for the new company. They are highly likely to allow you to do something with them, or at least give a grace period for spending them.

Additional: Some more information, some of it supposition, in this NY Times article, which seems to be based on an interview with the two CEOs, and is therefore presumably reliable:

• Dividend miles indeed absorbed into AAdvantage on a 1-for-1 basis.
• Maybe more free upgrades, and hence harder to get
• Maybe more elite tiers
• Different mileage airlines partners for those used to US Airways
• Different in-flight products (food, wi-fi)
• More routes, hubs, at least at first

You have two choices: (1) sign up for a US Airways mileage account, be sure that number is on the reservation, and then sit back and wait for the two mileage programs to be merged in 2015, at which point your US Air miles be added to your AAdvantage miles, or (2) credit the US Air flights to your existing AA account and earn the miles immediately. Unless you intend to also get a US Air credit card or purchase additional US Air bonus miles to take advantage of the sale, there is no point in (1), just go with (2) as it is the easiest. Just be sure your AAdvantage number is listed in the reservation and on your boarding pass.

Even though the two programs have not yet merged (this will happen in 2015), the two are partners, so you will earn both redeemable miles and elite-qualifying points and miles on US Air flights. See the AAdvantage partner page for US Airways for details.