I thought it was going to be iron, as it was getting close and I was doing (and still plan to do) large quantities of S2Es.
However, doing some heavy stocking for school supplies to poof on school days, I ended up harving extreme quantities of blue star flowers for blue dyes to poof in the tailoring school. And those dyes take 20 flowers each. Add to that stock for mixing SRs and I guess it's no surprise that BSFs became my first harvestable to hit the 1,000,000 harvs mark.
Current status: Harvest level 110, with only about 500k exp to go to level.
That's the full list. Green indicates items that are still regularly harvested. Red is stuff I almost never touch unless absolutely necessary these days (they've either been replaced with buying them or the item they're used for, or just are simply not used by me anymore). No dot means they do get harved on occasion, just not as much as the green dots. Those include things like flowers for creature food... not normally harved, but when I do, it's in large (10-20k batches) of them.
Every possible item that can currently be harvested in the game is represented above. Total harvests for this list is over 11 million.
A quick look at how the top 10 ended up being the top 10...
1) Blue Star Flower - As said above, primarily due to use of blue dyes to level tailoring, with a good amount needed for mixing SR potions. Two heavy uses.
2) Iron Ore - The usual, iron/steel bars to make S2Es. I also regularly mix a lot of energy essences (both for self-use in magic and poofing them in the engineering school as point defense).
I expect this will also hit the 1,000,000 as well very soon.
3) Sunflowers - There was a time I used tons of these for BRs while leveling potion. Potion has taken a back seat for leveling so I barely touch these now. They still get harved on occasion to stock LEs when I want to work on summoning stones.
They'll be back in heavy harv rotation again in the future, after I'm done with manu/eng gods and switch to magic/summon gods, which will mean tons of summon stone grinding, calling for tons of LEs.
4) Chrysanthemum - I've mentioned before that I heavily use HEs to level alchemy, so this is no surprise. I'm currently at 880k HEs mixed, so 827k mums is about right for that. (I do regularly mix other people's HE ings for them, explaining why I have a lot more HEs mixed than mums harved.)
5) Silver ore - 818k obviously doesn't cover the 880k HEs I've mixed, not to mention all the silver bars I've done. These days I heavily trade items for silver, or buy silver, so the need to harv it is drastically reduced. But it does still get harved, regularly.
6) Coal - No explanation needed... bars, bars, bars, bars, and, yes, bars.
7) Red Rose, 9) Red Snapdragons, and 10) Sulfur - From days gone by, when I used to do tons of FEs. Mixing these now is incredibly rare (a level 131 alcher doesn't get much out of them), so they're red-marked above. They still get harved on occasion but for the most part are avoided now, and will likely drop rapidly in the list over coming time.
8) Lilacs - Much higher than other magic ess ings, likely due to days of old when lilacs were used to get gc at the flower shop, plus harving them for a harv shop my guild back then used to run.
These days, I'm heavily stockpiling magic essence ings for poofing in the school on school days, so this along with impatiens and emeralds will continue to rise in harv count.