Which Encounter cards are worth keeping after defeating them?
I always keep in my deck all the new encounter cards and encounters that will earn me a token. There's still some room left over in the encounter deck, though, which needs to be filled out with encounters I've already beaten at least once.
Which encounters are good to keep around?
Obviously, ones which are purely beneficial, such as the Food Wagon, are good. What I'm mainly interested in are ones that involve some risk, but have a good gain that more than makes up for it. One example I've had a lot of luck with so far would be Deadman's Gorge. You fight one or two monster cards, and get three gain cards. That's a pretty good trade.
I tend to fill the rest of my desk with encounter cards that have the most variety of rewards. Not sure if that is the best strategy though.
Dead King's Hall - 3 gain cards, but you might get unlucky and also get a pain card.
Goblins - if you kill all the goblins, you will recover your equipment and gain some extra gold.