At the Oberwolfach meeting on Combinatorics on Words in 2010, the participants suggested a list of important open problems in the field.
Here is the list:
1. IsPiNormal?
10. PCP3Decidable
11. NivatConjecture
12. ReconstructionfromSubwords
13. HHPVProblem
14. SAdicConjecture
18. NumberofRightSpecialFactors
-- JeffreyShallit - 13 Oct 2010