When comparing Org mode for Emacs vs Trilium Notes, the Slant community recommends Org mode for Emacs for most people. In the question“What are the best knowledge base systems for personal use?” Org mode for Emacs is ranked 3rd while Trilium Notes is ranked 10th. The most important reason people chose Org mode for Emacs is:
Org mode started out as a simple outlining/note taking app. Then each outline heading can optionally be a TODO list item. And if you desire, you can add SCHEDULE and DEADLINE dates. (Schedule being the date you'd like to start the item.) You can customize the TODO states to add things like DELEGATED, WAITING, BLOCKED, etc.
Specs
Ranked in these QuestionsQuestion Ranking
Pros
Pro Can be as simple or as complex as you want
Org mode started out as a simple outlining/note taking app. Then each outline heading can optionally be a TODO list item. And if you desire, you can add SCHEDULE and DEADLINE dates. (Schedule being the date you'd like to start the item.) You can customize the TODO states to add things like DELEGATED, WAITING, BLOCKED, etc.
Pro Libre/open source
Pro Cross platform
Emacs runs on all platforms, Windows, Linux, OSX, even Android and IOS

Pro Exports data to PDF, LaTeX, HMTL and other
You can even build presentation or blog from your data

Pro Supports tables with formules (quite powerful!)
Pro Plain text data storage
Future-proof.
Pro Inline image displaying
Pro Free but copyrighted
Pro Fast interaction
Once muscle-memory sets in, can be much faster to use than a point & click program.
Pro Uses Emacs
Pro All apps
Pro Free and open source software
Pro Note encryption
Pro Excellent WYSIWYG interface
Pro Attributes that can be assigned to nodes and inherited
Pro Graph of node connectivity
Pro Note versioning
Pro Synchronization with a server
You can set up synchronization but you need a server to do this.
Pro Database storage rather than files
This enables the tool to do a lot of things that would be difficult with plain text file storage.
Pro Archival functionality
Cons
Con Obtuse documentation
The documentation assumes a level of understanding of basic Emacs usage that not all users may have.
Con Complicated to get started
Con Difficult to use as a database
For example, if you need to quickly populate client details on quotes, unfortunately its easier to find, copy & paste.
Con Not suitable for normal users
Not even a majority of software developers can be bothered to use Emacs (or VI, for that matter).
Con PDF export can be difficult
Latex assumes you're a (compliant) student, have to do a lot of research to get what you want out of it.
Con Uses Emacs (for those who prefer vi, menus, etc.)
Con Interface can be confusing
There is a fair amount of flexibility to the interface but it can also become confusing, especially when some parts are not necessarily simple to use. Most of the basic features nevertheless are intuitive.
Con Database storage rather than files
This makes it a little less simple to work with (also has benefits).
Con Not markdown
It will import and export markdown but it does not store content as markdown. This isn't necessarily a problem if you don't need it.
Con Synchronization requires use of Trilium's sync server
This can be problematic to set up unless you have a web server that will support the requirements of this.
