You can pick up torches, and click on creepy crawlers to get a reward. (Be careful to click directly on the creepy crawler; it's a small target.)
slug (at 50): 5 blue gems
Spider (at 100): 1 purple gem
Beetle (at 25): 1 blue gem
Roach (at 250): 1 purple gem
Slime (at 400): 5 purple gems
Snake (at 550): can't be hit with fire
Centipede (at 700): 1 green gem
Cobra (at 900): can't be hit with fire
Purple slime (at 1100): 2 green gems
Lizard (at 1300): can't be hit with fire

A bottle will appear on screen. If clicked, it will allow you to brew a potion. You can use a color twice or mix any two colors. Effects include:
income x2, speed x2, click x2, all bonuses, 1 blue gem, 1 purple gem, 1 green gem, bunch of dread, 2 potions
Each time the wheel resets, the effect of each color changes. If all 8 segments on the wheel have the same color, the last potion brewed will have 10 times the effect.

A petri dish will appear, and can be clicked to put it under the microscope. Move the syringe around the edge of the dish and click to fire. If a germ hits you, you fail the minigame. Once all germs are destroyed, you'll get a green gem.

A bar will slowly start increasing. Upgrade the generator to increase it faster. Once it has at least 3 bars, click the green screen to play tic-tac-toe against a chicken. It always starts, but it's not great at tic-tac-toe. If you win, you'll get a green gem.

Feathers will spawn at the chicken whenever you will a game of tic-tac-toe. Click on them, then the prisoner hanging from the wall. After 3 feathers, the prisoner will die and drop a green gem.

A bucket will spawn, and can be placed under a drip to fill with water. A full bucket can be used on the vine to let it grow. (The growth level of the vine does not change on reset.) Once the vine is big enough, it can grow fruit. You can feed fruit to prisoners to get 1 green gem. Once the vine is fully grown, adding more water will give 1 green gem.

Click on the flashing button on the device, and let it run for a while. (Will cost 3 bars from the generator.) It will produce a green ball, which can be clicked on to throw. It will bounce around the room and give a random bonus. Most likely is 1 green gem, though it can land in the generator to give extra power, or give 5 green gems if it lands in the bullseye on the wall, or a feather if it hits the chicken.

A switch near the door will allow you to drop the left-most cage. If you drop it on a wandering monster, you will imprison it, giving a bonus to the prisoner dread reward for a while. At 700 prisoners, the right-most cage can be dropped as well.

Three pieces of paper will appear. Click on them, then the chest, and enter the combination.

A flask will appear. Click on it, then on the flashing button next to the equipment to brew an enlarging potion. Click on the potion, then on something to enlarge it. Wait for a few seconds, and it will shrink down again, and give you 1 potion ticket. I recommend your assistant, or the spider, as neither of them will wander off.

After filling the bucket with water/ooze, open the freezer, place it in there, then hit the flashing button. (Will use 3 bars of power.) Once the bar fills up, open the door and remove the ice bucket. Release the bucket above the target critter. Bear in mind that the ice will travel down the screen, and you can hit more than one critter.
The lizard will give 5 green gems
The cobra will give 3 green gems
You can't freeze the snake
Other critters will give you 1 green gem. (Protip: use the spider. It doesn't move, so you can just wait until another critter is in line with it, and consistently get 2 kills without much waiting.)

Flip the switch to raise the monster. Will use all power bars. Will give 5 green gems after the monster finishes walking around.

Bit subjective, but whatever:

Auto collect (Good for getting more gems)
Hidden Spawn -30 seconds (Good for getting more gems)
Hidden Spawn -30 seconds (again)
Add warps to potion smash (This is common enough that you'll be getting warps reasonably often.)
Lab assistant income x2
Monster income x2
Bonus speed length x2
Bonus income length x2
Vine can grow 5 fruit (each is worth 1 gem)
Max out auto collect slots and spawn speed
Show total $/sec and +10% all
Add rare potion to potion smash (super rare, but whatever)
Auto clicker (mostly for the click achievement)
Double auto-click speed

The potion smash is mostly useful for getting warps. There are two main strategies here:

First, you could restock, smash one, and repeat. The benefit here is that you can rapidly cycle through rewards, and you don't need to put actual thought into things.

Alternately, you can see if there are any warps in the field, and choose to smash again if there are. Personally, I smash once more if there's 1 more warp on the field, and if there's 2 or more warps on the field, I smash until I find one. This doesn't provide as many rewards, so you won't be able to sustain this as well, but is a more efficient use of your time, making it more useful in the end game.

Thankfully, the rewards are good enough that this is almost self-sustaining once you have the 1-hour warp and a few auto collect upgrades.