This is a fully ready-to-use molecular visualization (molecular imaging) system for use in structural biology.
It allows to create high-quality three-dimensional images of both small molecules and biological macromolecules, primarily proteins.
About a quarter of all published images of protein structures in the scientific literature are made with PyMOL.

VisualFBEditor is an IDE for FreeBasic with a visual designer, debugger, project support, etc.
Allows the development of both console and graphical applications for different platforms Linux, Windows, Android.

Caliber is a library for cataloging e-books. Includes library management, eBook viewer and editor, and synchronization features for eBook reading.
Allows you to convert e-books to a dozen different formats and back.
Supports synchronization with almost all e-book reading devices (for example, Kindle, Kobo, Nook).
Can automatically pull news from a range of websites/RSS feeds, format the news into an e-book and download to a connected device.

FET is a program for automatically generating timetables for schools and universities.

Typically, FET is able to solve a complex problem in a maximum of 5-20 minutes. For simpler schedules, this may take less time (a few seconds in some cases). For extremely complex schedules, this may take longer and may take several hours.

Xournal++ - Create handwritten notes, sketches and journaling with a stylus. From solving a physics problem to keeping travel diaries. It can also be useful for adding annotations to PDF files.
Supports pressure-sensitive styluses and digital pens (e.g. from devices such as Wacom tablets, Huion tablets, XP Pen, etc.)
Possibilities:

Gobby is a collaborative editor that supports multiple documents in one session and multi-user chat. This means that it gives you the ability to edit files simultaneously with other users over the network.

Gramps is a program for genealogical research. It is an extremely flexible program that meets the needs of both the amateur genealogist and the serious genealogical researcher. Allows you to store, edit, and research genealogical data.
Has the ability to import GEDCOM files exported from many proprietary genealogy programs and can generate a large number of reports in many popular formats. This allows any piece of information to be entered directly into Gramps and any event to be manipulated across the entire database (in any order), helping the user research, analyze and find connections with the ability to fill gaps in relationships.

gImageReader is a simple interface for tesseract-ocr. Tesseract is probably the most accurate open source optical character recognition (OCR) software available and can recognize text in over 60 languages.

It supports automatic detection of page layout, but the user can also manually define and configure recognition areas. You can import images from disk, scanning devices, clipboard and screenshots. Supports multi-page PDF documents. Recognized text is displayed directly next to the image, and basic text editing is possible, including search/replace and removing line breaks. Spell checking of output text is also supported if appropriate dictionaries are installed.

Integrated application development environment (IDE) in the programming languages Java, JavaFX, Ruby, Python, C++, PHP, JavaScript/HTML5, Groovy and several others. To support development for mobile platforms (J2ME), you must install the NetBeans Mobility Pack separately.

In terms of quality and capabilities, NetBeans IDE is not inferior to the best commercial (paid) integrated development environments, supporting refactoring, profiling, highlighting syntactic structures with color, autocompletion of typed structures on the fly, many predefined code templates, and more.

A MIDI file player/game that displays the musical notes AND teaches you how to play the piano.

PianoBooster is a fun way of playing along with a musical accompaniment and at the same time learning the basics of reading musical notation.
The difference between playing along to a CD or a standard MIDI file is that PianoBooster listens and reacts to what you are playing on a MIDI keyboard.

To run Piano Booster you need a MIDI Piano Keyboard and a MIDI interface for the PC. If you don't have a MIDI keyboard you can still try out PianoBooster, using the PC keyboard ('x' is middle C), but a MIDI piano is really recommended.