There is actually quite a list of abilities that can in some way or another bypass invulnerability should the degree of control be sufficiently high:
Time Manipulation, Spatial Manipulation, Age Manipulation, Soul Manipulation, Mind Manipulation, Existence Erasure, Void Manipulation, Causality Manipulation, Probability Manipulation, Power Nullification, Death Manipulation, Plot Manipulation, Logic Manipulation, Information Manipulation, Mathematics Manipulation, Higher Dimensional Manipulation, Chaos Manipulation, Law Manipulation
Depending on how the specific ability and the invulnerability work: One Hit Kill, Physics Manipulation, Petrification, Transmutation, Magic, Absorption, possibly Matter Manipulation, possibly Antimatter Manipulation
This should have been all.
NOTE: Some of them may be debatable or depending on the situation and how the powers in question work. Should the invulnerability of the character in question be limited to his skin/armor/shell even more abilities will work. Also note that invulnerability is sometimes tied to certain conditions (activation requirement, limited duration, etc.). In that case skill, strategy, preparation, intelligence and/or experience can be used in order to exploit those weaknesses to get around the invulnerability.