When comparing Gingko vs MDwiki, the Slant community recommends Gingko for most people. In the question“What is the best cross-platform note-taking app?” Gingko is ranked 20th while MDwiki is ranked 70th.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro You can customize colors
Pro Allows focusing on one piece of information at a time
Since Gingko documents are "trees", they are always organized on the go. And since everything is written in cards, it is possible to focus on one chunk of content at a time.
Pro Easy to overview
Despite the complexity of the tree structure, it's always clear where you are, and how to quickly add your thoughts.

Pro Markdown support
All formatting is done via Markdown.
Pro Non-linear
Non-linear notetaking allows you more flexibility, freedom and creativity.
Pro Possibly more secure on web server
Due to the lack of a built-in editor MDwiki may be less susceptible to spam and defacement compared to other options when served from a web server.
Pro Doesn't require a web server
MDwiki is a self-contained JavaScript app that is very fast and can run in some web browsers such as Mozilla Firefox.
Cons
Con Limited free version
The free version is limited to 100 cards and 10 documents. Depending on how you use it, this might not be enough.
Con External program must be used for editing
A separate program must be used to make changes to documents as MDwiki lacks a built-in editor.
Con Requires additional permissions in Google Chrome
Supposedly, you can get it to work in Google Chrome by modifying JavaScript permissions, but these same changes may decrease security.
