data generation and analysis:
CIPRES (powerful web-submitted phylogenetic analysis)
PartitionFinder (infer models of sequence evolution across many partitions)
Genomic Diversity Facility @ Cornell Univ. (Genotyping by Sequencing) 
Center for Anchored Phylogenomics
ipyrad (user-friendly short-read assembly and SNP-calling) 
PCO-MC (multidimensional clustering)
Rambaut homepage (Se-Al, BEAST suite, Tracer, FigTree)
GenoDive (clustering, hybrid index, etc.) 
Beocat (Kansas State Univ. HPC cluster)

herbaria and collections:
Index Herbariorum (searchable database of herbaria worldwide)
Pryer Lab Fern DNA database 
Tropicos (Missouri Botanical Garden specimen database)
Index to Plant Chromosome Numbers
Online Manual of North American Grasses

misc. helpful stuff:
Institute for Botanical Training (learn plants in the field from ultra-knowledgeable folks!)
EarthPoint (interactive township/range interface with Google Earth)https://www.phylo.org
Beck Lab Links