To find the percentage of gingerbread cookies, we can use the formula:
\[ \text{Percentage} = \left(\frac{\text{Number of gingerbread cookies}}{\text{Total number of cookies}}\right) \times 100 \]
In this case, Bob ordered 5 gingerbread cookies out of a total of 100 cookies. Substituting the values into the formula, we get:
\[ \text{Percentage} = \left(\frac{5}{100}\right) \times 100 \]
Calculating this gives:
\[ \text{Percentage} = 0.05 \times 100 = 5% \]
Thus, the percentage of the cookies that were gingerbread is \( \boxed{5%} \).