Of the various methods of labeling biomolecules, fluorescent labels are advantageous in that they are highly sensitive even at low concentration and non-destructive to the target molecule folding and function.
Green fluorescent protein is a naturally occurring fluorescent protein from the jellyfish Aequorea victoria that is widely 
used to tag proteins of interest.  GFP emits a photon in the green region of the light spectrum when excited by the absorption of light.  The chromophore consists of an oxidized tripeptide -Ser^65-Tyr^66-Gly^67 located within a β barrel.  GFP catalyzes the oxidation and
only requires molecular oxygen.  GFP has been modified by changing the wavelength of light absorbed to include other colors of fluorescence.  YFP or yellow fluorescent protein, BFP or blue fluorescent protein, and CFP or cyan fluorescent protein are examples of GFP variants.  These variants are produced by the genetic engineering of the GFP gene.
Synthetic fluorescent probes can also be used as fluorescent labels.  Advantages of these labels include a smaller size with more variety in color.  They can be used to tag proteins of interest more selectively by various methods including chemical recognition-based labeling, such as utilizing metal-chelating peptide tags, and biological recognition-based labeling utilizing enzymatic reactions.  However, despite their wide array of excitation and emission wavelengths as well as better stability, synthetic probes tend to be toxic to the cell and so are not generally used in cell imaging studies.
Fluorescent labels can be hybridized to mRNA to help visualize interaction and activity, such as mRNA localization. An antisense strand labeled with the fluorescent probe is attached to a single mRNA strand, and can then be viewed during cell development to see the movement of mRNA within the cell.