This might be well known, but I've never really seen discussion of it and just used it to my benefit, so:

Situation: Attempting to book a flight to Perth. Search gave me SFO→SYD in L, SYD→PER on Qantas in Q. Suboptimal. Plenty of W available on the United flights (and even R for the dates I was looking at), so the normal thing I'd then do is use advanced search and choose W as the specific fare class. But in this case that didn't work - there was no W availability on Qantas. And then I noticed something that I'd never really considered before - you can enter a list of fare classes. One advanced search later for W, Q and I had SFO→SYD in W and SYD→PER in Q.

As far as I can tell it'll pick the cheapest fare class from the list for each flight, so it's probably most useful for dealing with partner flights that have different prioritisation. There are cases where it's useful for domestic+international itineraries that price out with the domestic portion as a separate fare basis - if you're ending up in G on the domestic portion and L on the international, searching for W, G should leave you with the international portion in W (because there's no G availability) and still put you in G on the domestic part. Searching purely for W would force both portions to price out in W.