As an aside, stomach flu is not the flu; it is gastroenteritis (inflammation of stomach and intestines which can be caused by a number of factors).
Technically speaking the difference between the flu and a cold is the pathogen. Flu is caused by the influenza virus. Colds are caused by a different set of viruses including rhinovirus (10% to 40% of colds), coronavirus (20% of colds), and respiratory syncytial virus (10% of colds).
A terrific chart from the Illinois Department of Public Health (Figure 1) compares the flu to the cold. The two share many symptoms such as runny or stuffy nose, sore throat, cough, body aches, and fatigue. These tend to be more severe in the flu with a faster onset (within hours rather than days).
In addition, flu can cause fever (100 - 103 oF) which is rare in colds, and in kids flu can cause nausea, vomiting and diarrhea which are uncommon in colds. Moreover, extreme exhaustion is "early and prominent" in flu whereas it is never found in colds. Also headaches are common in flu but rare in colds.
The biggest and most important difference between the two is in the area of complications. Flu can lead to pneumonia and bronchitis which can cause death if severe enough and not treated properly. Colds do not have these complications. In addition, flu can aggravate an existing chronic illness (such as congestive heart failure or chronic obstructive pulmonary disease). This is why flu is much more deadly (~25,000 people die each year from flu-related causes in the U.S.) than colds which seldom lead to serious health problems.
There is no vaccine or treatment for colds; you can only treat the symptoms to alleviate the suffering. There is a flu vaccine which is reasonably effective (reduces risk by about 60%), and their are anti-viral drugs such as Tamiflu given to patients whose condition may be endangered by the flu.
In summary, a fast onset, fever, exhaustion, and headaches are indicators that you have the flu rather than a cold.
Figure 1. Chart from the Illinois department of public health comparing the flu to a cold.

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