Problem (Workup Nightmare #1): Upon combination of organic and aqueous solutions, a gooey or insoluble precipitate appears, which floats between the two layers and obscures the border.
Solution: Keep washing with water until most of the goo is removed. Then use copious drying agent, and with luck, the goo will be absorbed and you will be able to filter it away.

Problem (Workup Nightmare #2): When an aqueous solvent is added to the diluted reaction mixture, an emulsion forms. All efforts to resolve the layers fail, your solution has swollen to gargantuan proportions, and you can't find or can't lift a separatory funnel large enough to hold it
Solution: See How To Manage an Emulsion.

Problem (Workup Nightmare #3): During Acid/Base Workup, the expected precipitate does not form.
Solution: See Acid/Base Workup.

Problem (Workup Nightmare #4): Upon addition of aqueous bicarbonate, the organic layer becomes a graceful fountain, coating the inside of your fume hood.
Solution 1: When you repeat the procedure, add aqueous bicarbonate carefully, shake gently, and vent the separatory funnel often.
Solution 2(abundance of caution; submitted by Valentin Geiger): Transfer the organic layer to a flask (Erlenmeyer or round-bottom) and add the aqueous bicarbonate to this, with vigorous stirring. Continue to stir vigorously for 10 minutes after complete addition of the aqueous phase. This will allow the mixture to degas a large portion of the dissolved CO2. (Note that the larger the reaction, the longer it should be stirred. 10 minutes is likely not enough for more than 250 mL of total volume.) Transfer the mixture (back) to the separatory funnel and continue as normal.

Problem (Workup Nightmare #5): Addition of aqueous solution to your black organic reaction mixture leads to a uniform black mixture. The solution in the addition funnel is opaque, and you can't see the border between the organic and aqueous layers.
Solution 1: Try adding ice, which will float on the water, between the layers.
Solution 2: Try adding a septum or polypropylene cap into the separatory funnel. These typically sit at the phase interface. Note that many solvents can extract materials from septa (usually this is inconsequential), thus a polypropylene cap is generally preferable.

Problem (Workup Nightmare #6): The aqueous solution you use to wash the organic layer turns yellow, orange, brown or pink- the first ten times you try it.
Solution: If the color is caused by excess halogen reagent from your reaction mixture, try washing with sodium thiosulfate. The solution should become instantly clear- if it does not and you still suspect halide, try stirring vigorously in an Erlenmeyer for 10-15 minutes to complete the destruction of halogen molecules.

Problem: (Workup Nightmare #7): After workup, you can't find your product.
Explanations and Solutions:
- Your product may be soluble in the aqueous layer- check it (you still have it, right?)
- Your product may be volatile: check the solvent in the rotovap trap.
- Your product may have gotten stuck in filtration media- if you had a filtration step, suspend the solid in an appropriate solvent and TLC the suspension.

We thank Professor Jeff Manthorpe (Carleton University) for helpful input to this page.