A Perfect Reaction : Combination of reactants is simple, and goes smoothly. The reaction is homogenous, and stirs easily. You can follow the progress of the reaction by periodic analysis using simple TLC or GC, and can stay with the reaction until it is complete. All the starting material is consumed, and one new product is formed cleanly (aka "spot to spot").

A Nightmare Scenario : The reaction takes hours to complete: however, the product is unstable and decomposes slowly under the reaction conditions. Progress cannot be monitored by TLC.

Step by step:

Save a small sample of each reactant in a vial, for TLC comparison. An NMR sample works nicely, or a milligram or so in solvent.
Follow the literature procedure exactly. Proper execution is essential- see selected topics below for more information.
Take a TLC of the reaction as soon as addition is complete. Co-spot with your reactant sample(s).
Record all observations and times in your notebook.
TLC or GC the reaction at regular intervals. The appropriate interval to employ will depend on the reaction rate- (e.g. every 10 minutes, or 30 minutes, or every hour). Always co-spot with reactant(s).
Do not leave your reaction before it is done or there might be repercussions. See leaving the lab for exceptions.
When one of the reactants has been consumed, quench the reaction immediately.

Tips

General

PAY ATTENTION. Many cases of experimental failure are repercussions resulting from inattention, or from leaving the lab while a reaction is underway.
BE PREPARED. When you start an experiment, the clock starts ticking. Make sure everything is ready beforehand.
MONITOR REGULARLY. Many students do not track their experiment closely enough.
If the reaction stalls, sometimes it is a good idea to add more reagent to ensure complete conversion. However, this is not recommended the first time through.
If no reaction occurs, try raising the temperature.
If product appears to be decomposing faster than it is forming, consider quenching the reaction before reactants are completely consumed. This may be the best way to maximize your yield.

Stirring

If stirring stops during a reaction, all bets are off. It is very important to stir continuously throughout an experiment. If your reaction is heterogeneous, it must be stirred very vigorously to ensure efficient mixing.

Stir Bars

Cylindrical:Long and thin bars that are excellent for Erlenmeyer flasks, but may spin irregularly in a round-bottom. The short cylindrical bars sometimes fit in a round-bottom and spin fine.
Football: Bars shaped to fit in a round-bottom flask. Normally available for 25 mL flasks and larger.
Fleas: Very tiny cylindrical bars good for 10 mL or smaller flasks, vials or test tubes.

Overhead Stirring

When a stirbar simply does not do the job, mechanical stirring is necessary. An overhead stirring apparatus is typically employed. Situations when overhead stirring may be required: high viscosity solutions, large scale reactions, or in heterogeneous reactions when a stirbar becomes mired in gunky, gooey, or otherwise insoluble material.

Troubleshooting

If you experience problems stirring, here are some things to try:

Move the bottom of the flask closer to the stir plate.
Use a bigger stir bar.
Use a larger or more powerful stir plate (not all plates are created equal).
If your stir bar gets stuck somehow, pick up the flask and swirl it until the bar is free, or pry it free with a pipette or spatula. These kinds of reactions require constant surveillance. If you are having this kind of problem, you might want to consider using a mechanical stirring apparatus.
If your reaction is very large, a stir bar may not mix it efficiently. It might work better if you used a mechanical stirring apparatus.

Notes

Temperature Control: Resources

Synthetic organic experiments are conducted at temperatures ranging from -90 degrees to 200 degrees Celsius. It is important to know how to achieve and maintain the correct temperature for a reaction, especially over long time periods. Temperature should be monitored with a low-temperature alcohol thermometer.

Low Temperature Cooling Baths

Cryocool: If you have access to one, a cryocool can maintain a reaction at a set temperature (typically -40 to 20 degrees) for a long period of time.
Ice/Salt: -15 to -5 degrees
Dry Ice/Acetonitrile: -40 degrees
Dry Ice/Acetone: -78 degrees
Liquid Nitrogen/Dichloromethane: -92 degrees

See Also: The Complete List on the Hoveyda Group website.

High Temperature Reactions

Hot plate/oil bath apparatus with internal temperature control.
Solvent reflux: temperature will be the boiling temperature of the solvent.
Oil bath: Mineral oil polymerizes at ~150 degrees; for higher temperatures switch to silicone oil or a heating mantle with sand (see below).
Heating mantle full of sand controlled by a Variac. Sand is less messy than oil and high temperatures are easy to attain. Put a thermometer in the sand and then experiment with the Variac until you achieve the correct temperature.
Hot plate/water bath. Sometimes convenient for gentle heating (35-80 degrees).

The Reaction: Analysis I