When comparing vimwiki plugin for vim vs Tomboy, the Slant community recommends Tomboy for most people. In the question“What is the best cross-platform note-taking app?” Tomboy is ranked 14th while vimwiki plugin for vim is ranked 23rd. The most important reason people chose Tomboy is:
All the components are free, opensource, and allows self-hosting the sync server.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Internal link makes it easy to create a knowledge network
Pro Comfortable for Vim users
Has a very minimal learning curve for people already used to Vim, as the preset shortcuts are very easy to learn and don't conflict badly with other Vim behaviors.
Pro Free and open source
All the components are free, opensource, and allows self-hosting the sync server.
Pro Can be extended with add-ins
If Tomboy doesn't have the features you want out of the box, you may be able to find them here as a plug in.
Pro Lightweight
Cons
Con Limited to use with vim only
vimwiki is a plugin for vim, so you won't be able to make use of it if you're not a vim user (and don't want to be).