KAT: k-mer counting and comparison tool, capable of comparing multiple libraries.
khmer: probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization.
Jellyfish: very easy to operate, but certainly not the fastest k-mer counter out there
FASTK: Presumably the fastest counter, but it is unable to count repetitive kmers; using a workaround and modified version of genomescope called Genomescope.FK the genome size estimates are still in the right ballpark.
Kmer spectra analysis tools
GenomeScope - a kmer spectra analysis tool suited for polyploids as well
tetramer - fitting pamaters to k-mer spectra of allotetraploids
findGSE - an alternative model for fitting genome sizes
QC of genome assembly
KAT - KAT can plot the k-mer spectra with colouring by the frequency of the given k-mer in assembly, which is a very smart way how to inspect collapses of paralogs and duplicates.
Merqury - Just like KAT but also made for trio data and coloring the assembly by the maternal and paternal contribution