Before I had to move overseas for work, I ran my games in person rather than online and I had all kinds of 2D and 3D terrain. I find that I don't use it that often. Mainly I use it for set-peice encounters that I know the players will get to and that I can prepare before the game. My prep is not usually actually having everything set up but having all the peices selected and ready to place down.
Which is funny, because most of this stuff I bought for on-the-fly setups. I just found that digging for the right pieces was too time consuming no matter how will I organized things. I end up just drawing "scatter terrain" with wet erase markers on the dungeon tile or battlemat.
The scatter pieces that get the most use are Arc Knight 2D double-sided flat plastic minis. I have all my arch-knight stuff, along with some printed 2D minis on card stock cut out with my Silhouette paper cutter organized in #10 envelopes with what they contain written in thick black marker on the front side of the envelop. I have s wide shoebox that is the perfect side for holding #10 envelopes and I have all the envelops containing the 2D minis (creatures, NPCs, and terrain items) organized alphabetically. So it is pretty easy to find the envelope for "trees" or "wagons" or "campsites".
For VTT games I would only uses scatter terrain tokens if they are items that moveable and which characters may move as part of their tactics. Otherwise the dungeon dressing is just part of the background battlemap image.
