SDS in the staining solution:  Most users save and re-use their staining solutions.  This is fine for a couple of cycles, but over time enough SDS elutes from the gels to accumulate to significant levels in the staining reagent.  SDS interferes with the binding of the dye to the proteins, resulting in bands that are fainter than expected.  There is no practical way to regenerate the staining solution-  discard it and make a fresh batch.

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To prolong the life of your staining solution, wash the gels briefly in water, or pre-fix the gels in methanol:water: acetic acid prior to staining.
Old dye or staining solution:  Coomassie Blue R-250 is not stable indefinitely-  older batches of dye or staining solution may show enough dye degradation to limit staining.  In some cases, the solution will show a dye precipitate, and staining can be improved by filtering the mixture.
Staining time too short, or too little agitation:  It takes time for the dye to penetrate the gel-  the speed of this diffusion is increased substantially by agitation during staining.  In general, you should not expect your darkest bands to be darker than the background when you begin destaining-  ie the protein bands won't grow darker as the dye is eluted from the gel.

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Bands too diffuse to see, due to poor electrophoretic separation:  Always use fresh, high-quality matrix and buffer components-  poor reagents will result in electroendosmotic band spreading, which can dramatically lower band intensities.