I picked a system (Rubbermaid in my case) and bought a couple sets that covered all the sizes I was likely to use. That way all the lids match, everything nests in the cabinet, etc. Then I gave my daughter (who was just starting out) first pick of the odd stuff, tossed what didn't have lids etc.
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I chose Rubbermaid bc they were affordable and I don't reheat stuff in them (plastic). Heard good things about the glass systems though.