When comparing Notepad++ vs WinMerge, the Slant community recommends WinMerge for most people. In the question“What is the best tool for resolving conflicts when merging file changes?” WinMerge is ranked 4th while Notepad++ is ranked 8th. The most important reason people chose WinMerge is:
You can quickly copy changed lines (or files in folder comparison) in both directions with keyboard shortcuts. You can edit the files as well, with syntax highlighting of some languages.
Specs
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Pros
Pro Syntax highlighting for a wide variety of languages
Notepad++ has built-in support for syntax highlighting for a wide selection of programming languages.
Pro Light and fast
Notepad++ is a very light program that starts almost instantly. This makes it a great text editor for users that want something that will start the second they open it.
Pro Extendable via plugins
A list of hundreds of plugins is maintained.
Pro Portable
You can get a portable version of N++ and put it on a flash drive or your dropbox account and have your editor, configured the way you like, at any computer that you are on.
Pro Free under GPL
Notepad++ is licensed under GPL, which means it is free/open source software that you can use freely.
Pro Regex replace in selection, active tab, or all tabs
In Notepad++, the user can utilise regular expressions to quickly modify text across multiple files.
Pro Persistent documents, even after exiting the application
If you close Notepad++ (npp), your documents remain even if you haven't saved.
Pro User defined language syntax support
You can define your own custom syntax highlighting rules (or add support for others) .
Pro Easy to use and admin
Very easy to use and personalize.

Pro Multi-line editing
While it is disabled by default, when enabled, it is possible to edit more than one line at a time. This is helpful in many situations.
Pro Split screen
The user can open and edit files in multiple screens within the editor window.
Pro Supports Markdown
If you have the Plugin Manager installed you can search for MarkdownViewer++ and install it via that plugin.
Pro File edition
You can quickly copy changed lines (or files in folder comparison) in both directions with keyboard shortcuts. You can edit the files as well, with syntax highlighting of some languages.
Pro Compare folders and files
Can show what files has been changed in a folder, allows comparing files in tabs.
Pro In line comparison
Can show differences within a line.
Pro Free & Open source
Winmerge is a free and open source tool.
Pro Good shell integration
Select two files and compare them. Alternatively, select one file, navigate elsewhere, select the other file to compare.
Also supports drag'n'drop of files / folders from Explorer.
History of past comparisons.
Pro Lightweight, quick startup
Binary is less than 3 MB, so it starts quickly
Pro Filters
Can filter out files for folder comparison, lines for file comparisons, with regular expressions.
Options also allow to ignore whitespace differences, white lines, case change, line-ending changes, etc.
Pro Good navigation
Keyboard shortcuts (and toolbar buttons) to navigate to next (previous) difference, side panel shows a map of the files with changed lines and allows to jump to a given place.
Pro Good detection of moved lines
Detects when a block of lines has been moved in the file and shows the relation.
Cons
Con Windows-only
While it can run in Wine, it is native only to Windows. Linux users will have to use Notepadqq instead.
Con Settings confusingly scattered
Examples: try to change the tab size or used font.
Con Annoying update notifications upon start-up
Annoying update notifications tend to pop up upon start-up after not having used the app or machine for a few days. At the same time, they can be easily turned off.
Con Outdated UI
Only the text area can be themed, and it doesn't have as many features as browser-based text areas.
Con Limited new syntax support for new languages
It may be hard to find good plugins for relatively new languages.
Con Session backups not enabled by default
Unsaved tabs will be lost when Npp crashes, unless you first enable the session backup option.
Con User defined language doesn't support triple quote strings
It also doesn't support triple hashed comments. Both styles are overridden by their single character single line version.
Con Windows only
It's only available for Windows. No Mac or Linux versions available. It is possible to run in Linux via WINE, although a bit unstable.
Con Development is spotty
The latest version (2.16.0) was released in November 2018. Before that the last official release was made in 2013. The 2.16.0 is actually one of the two forks (Winmerge-v2-jp) that were kept maintained throughout the years, it just got named as the official release.
The other fork, WinMerge2011 is still being actively developed too. It's on par with the historical version, and has additional features such as showing only differences and a 64-bit version.
An 'official' list of forks is maintained here.
Con No 3-way merge
Cannot merge 3 files, can do only comparisons by pairs.
Makes it unsuitable for merging operations, still useful to compare two versions in the history.
