I recently booked a complex multi-airline itinerary on Expedia.com, and was happy with the support provided by Expedia for entering the FFP numbers. It was very easy to select a different FF account for each of the different legs. Expedia stores account numbers as part of your profile - it includes 39 of the FFPs - so you never need to re-type the account number.

I also noticed that there's a "Update Frequent Flyer Number(s)" option as part of your itinerary, which allows you to change your selection after purchasing the ticket.

There are a few glitches. For example, you can select a FFP for a flight operated by a non-participating airline. In other words, Expedia does not verify partnerships. But other than that, it seems that among the big online travel agents, Expedia has the best FFP support.

I wonder if other FTers share this view. Also, what other features for frequent flyers would you appreciate when booking a flight?