The best replacement for wood filler is wood putty.

The best alternatives to wood filler are rated as following:
★★★★★  wood putty
★★★★  spackle
★★★★  bondo
★★★★  caulk
★★★  putty
★★★  epoxy
★★  grain filler
★★  wood glue
★  joint compound
★  plastic wood
★  spackling paste
★  painters putty
  polyfilla
  spackling
  drywall compound
  caulking

Your alternative for wood filler is not listed? Suggest!
Speaking about wood filler, one probably shouldn't forget about sawdust.

Other search terms related to wood filler and their ratings are:
★★★★★ sawdust
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Google Trends

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wood filler
wood putty
spackle