Value
The numismatic worth of the penny that you want to clean is the single most important variable when it comes to cleaning pennies. If you think that the penny may be worth significantly more than its face value of one cent, do not clean it. Cleaning a valuable penny will only lower its overall worth. This may seem to contradict the importance of physical condition on the value of the coin, but most cleaning techniques actually do more harm than good to the surface of a penny. Shininess is not the only indicator of good physical condition.
Coin Composition
Most pennies are composed of zinc and copper. However, for many years, "Indian Head" pennies were made out of bronze and during 1943, pennies were made out of steel and zinc. While composition isn't that important when dealing with most mild, household cleaners, it does become a concern when using stronger industrial-level cleaners --- many of which work very well when cleaning pennies. Always check the composition of your pennies and the specific uses of your cleaner before cleaning your pennies with strong cleaning agents.
Soaking Pennies
If you are soaking coins in soapy water, cola, vinegar or any other liquid in order to remove dirt, you will want to soak the coins one at a time. If you place multiple coins in a single bath, some of the grime from one coin may end up transferring to another coin. Length of time is also an important variable when soaking pennies. Certain cleaners --- including lemon juice --- will turn the coin black if it is immersed in the liquid too long. As a general rule, remove the coin from its bath when it looks clean.
Smell
Smell may seem like an odd variable when it comes to cleaning pennies, but some of the most common penny cleaning materials have very strong, often disliked scents. Ketchup is an extremely common condiment that can be used to clean pennies, but it will impart a tomato-like scent to the coins. Vinegar and salt has the same problem. Some of the stronger cleaners may impart a bad smell to the pennies as well.