There are quite a few things from Star Trek Online, which have been removed and that I do miss...
Memory Alpha, because it was such a fun place to visit.
There was an STF, where you fought through an armada of ships, to reach some huge X's above a planet.
Mine Trap, which was without a doubt, my favourite STF.
Starbase 24, which was incredible for levelling.
I know the removed episodes like the "Lost Dominion" Arc are still available in the "Available" section, but I don't understand why they're not part of the episode tree (and that unless you know to look for them, you won't find them).
...what do you miss?