Links that indicate their relationship type. For example, here's a wiki-style link that includes a relationship qualifier (instead of "OTHER-NOTE", insert your usual link ID format):
In this example, "refutes" indicates that the thought in the current note refutes/rejects the thought outlined in that other note (which has the ID "OTHER-NOTE"). Others have already thought up an entire set of qualifying properties (see CiTO properties) which could be used. If more software starts to support qualified links (aka "semantic citations" or however you call them) like this, this would open up entire new possibilities.
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Is there a benefit to Luhmann IDs vs. Date/Time IDs?, [no date]. Zettelkasten Forum. post 
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> The only relation within a boundary calculus is that of Containment, a minimal conceptual basis consisting of one binary relation. The contains relation is quite general. When expressed within logic, containment can be interpreted as implies. When expressed as a network, containment is directly-connected-to. When expressed as a set, it’s called is-a-member. When expressed as a number, it is successor. When expressed as a map, it’s shares-a-common-border. Within the context of a pile of blocks, contains becomes supported-by. When seen as a family relationship, it is parent-of. When described as an abstract mathematical structure, it is a rooted tree. All of these metaphors share a collection of common characteristics that are concretized by the properties of physical containers. The fundamental concept underlying containment is Distinction: a container distinguishes inside from outside.