A few additional options:
1. You are discarding two big cards for your Outpost turn (e.g. two Minions, two Apothecaries, two Libs, two Tr in an early Alchemist deck, etc.) and then playing a Moat. Discarding a junk card first means you have a 1/3 chance of drawing both your big cards. Leaving any random junk card makes it 100% than you will have at least one of them in your 3 card hand.
2. You expect to be hit with a Masquerade next turn and want to be sure to have the junk in hand to pass.
3. You have 5 Treasuries or other means of top decking 5 cards during cleanup, leaving the junk on top makes for good Swindler/Knights/Rogue defense (it also works well against Pirate Ship/Thief/Noble Brigand a bit more situationally). You can also use this to stack the deck so your opponent's Tribute hits junk instead of action (really hilarious to do with curses, people HATE it when you perpetually top deck the two curses you bought against their Tribute engine).
4. You expect to be hit by a Minion next turn and would rather have it in the discard than in your 4 card hand.
5. Rebuild and Farming Village can follow the same logic as Sage/Golem - if you leave the card on top before play, you will be able to discard after drawing the card you really want (e.g. Rebuild on top - name Estate, reveal past your junk, shuffle up a new draw deck, reveal & Rebuild a Duchy into a Province, discard the junk).
6. You want to Island/Native village away the junk next turn or this respectively.
7. You need discard fodder for the next card down next turn. E.g. you know you will draw junk/Hamlet/Smithy, leaving the junk lowers the odds of having to discard something strong to the Inn. E.g. you know next hand will be junk/Tac
8. You want to be able to play more cards without digging into the deck. E.g. you played Spy, drew Scout (thanks to Swindler) and want to play the Scout to get free Peddlers. Discarding the junk increases the odds that your Scout will turn up Nobles that you don't want this turn (you have no other cash/buys in deck).