What are the cases in which each of those is used? Can you give more detailed examples and differences in meaning and usage than the ones I found below if there are any?
Here's what Google says:
over the years: during several/some/many years (Merriam-Webster)
for years: for a long time (Cambridge)
throughout the years: during the whole of [a certain] period (Collins)
For example, I have a sentence:
"... after all the [lies] he's fed himself over the years."
Is that the appropriate usage?