Having had two games where this was worth considering, I'd like to know who else has done this much. Basically, when have you used a top-decking ability to deliberately put junk on your deck as protection against an Attack or other card an opponent might play? One of my favourites is in games with Secret Chamber and Scrying Pool - they're already pretty nice to start with, since you can use one to feed the other, but if you've got the Chamber in hand when your opponent plays their Pool there's nothing nicer than pulling up a couple of Victory or Treasure cards, then putting a junk card and a spare Action back on top. Almost invariably they'll see the junk card and leave it there, letting you get rid of it with a Pool of your own and moving straight onto a guaranteed Action. Alternatively, you could always put a card that they're likely to make you discard that you didn't actually want in the first place - like a Gold you don't want to draw until the end of a run of Pools.
Another case I can think of is using top-decking with Scheme, Herbalist or Watchtower to deliberately put a bad card into your hand to use against, say, Masquerade. Of course it's most helpful when you know that your opponent is almost certainly going to play the card in their turn, or if you have an alternative use for it (or a way to make it not matter that it's in your hand).