What's the difference between flagella and 'pili' in prokaryotic cells?
are the pigments presented by photoautotroph organisms similar to chlorophyll?

Q1. The main difference between flagella and pili in a prokaryotic cell is their length. Flagella are long and thin, whip-like appendages that extend from the interior of the prokaryotic cell. There are much fewer flagella than pili on the prokaryotic cell. Pili are short and hallow, hair-like appendages from the surface of the cell. They do not extend from the interior of the cell.
Flagella are made of protein flagellin while pili are made of protein pilin.
Flagella can be found in both Gram+ and Gram- bacteria while pili can be found only in Gram- bacteria. 
A function of flagella is motility. Pili can perform motility but are rather responsible for attachment and genetic exchange.

Q2. Photoautotrophic organisms contain pigments that help them absorb the light of certain wavelength so they can make their own food (because they are autotrophs) in the process of photosynthesis. There are different types of pigments and it is hard to say if they are similar to chlorophyll or not. Because they do the same function, but also they differ in chemical composition.