The best replacement for taxonomy is ontology.

The best alternatives to taxonomy are rated as following:
★★★★★  ontology
★★★★★  systematics
★★★  phylogeny
★★★  folksonomy
★★  classification
★★  cladistics
★  metadata
★  webb\u0027s depth of knowledge
★  category
★  cck
★  facets of understanding
★  typology
★  navigation
★  depth of knowledge
★  tags
  lexicon
  bloom taxonomy
  phylogenetics
  taxonomist
  revised bloom\u0027s taxonomy
  information architecture
  bond\u0027s cultural taxonomy
  category wordpress
  nomenclature
  webb's depth of knowledge
  dok
  hierarchy
  binomial nomenclature
  controlled vocabulary
  marzano\u0027s taxonomy
  marzano's taxonomy
  ecology
  six facets of understanding

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Speaking about taxonomy, one probably shouldn't forget about more traditional taxonomy.

Other search terms related to taxonomy and their ratings are:
★★★★★ more traditional taxonomy
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Google Trends

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taxonomy
ontology
systematics