I guarantee that the best open-source plasmid editor/viewer will become a ubiquitous piece of software in every university. And eventually, even, homes.

http://www.mekentosj.com/science/enzymex - guys who made papers made part of it. Nicest interface, but missing lots of features.

http://biologylabs.utah.edu/jorgensen/wayned/ape/ - is what everyone uses. It's old. Functional, but missing SO much of what's possible.

https://www.dna20.com/genedesigner2/ - made by the best in the industry. Look at that shit.

http://bioclipse.net/screenshots - opensource, but look how difficult. How not right.

The rules are straightforward. It's a lot like writing out an API. A good manipulator of well-documented data structures.