What are useful online tools for cloning/genetic modification/molecular techniques?

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Francisco Benítez de la Fuente Popular answer

Benchling. It's basically a free, online version of SnapGene. I have been using it for 2 years now and I cannot complain.

Alexandra Johnson

NEB has some nice things for cloning:

https://www.neb.com/tools-and-resources/interactive-tools

Personally I only really use the NEBuilder tool for designing primers for Gibson Assembly but I know other people in my lab use the double-digest finder for restriction cloning.

Primer BLAST is my favorite tool for primer design since it checks for primer specificity against a given genome:

https://www.ncbi.nlm.nih.gov/tools/primer-blast/

addgene.org isn't really a tool, but it's my go-to when I need to find plasmid sequences since they also carry maps/sequences even for plasmids they don't have in their physical repository.

Francisco Benítez de la Fuente

Eugen's answer just reminded me of another one: http://www.molbiotools.com/restrictionanalyzer.html

Does restriction digest analysis and shows a mock gel of all the predicted products, I've even used it on whole bacterial genomes to figure out the best enzyme to give me a good range of product sizes for Southern blotting. It also has options for dam/dcm methylation in case the enzyme might be methylation sensitive when the DNA is extracted in some E. coli strains.