There are a wide variety of citation management systems available, and each has its strengths. Try out several to determine your personal preference. Many offer syncing of PDF libraries for a fee, and some systems are free while others are paid software. Both web-based and software systems are included here.
Entering multiple fields for both Japanese and romaji text is a major challenge in these citation managers. The only systems that are customizable enough to effectively do this are EndNote and Bookends; each of these has many customization possibilities and are manipulated in different ways. Both are paid desktop software.
Project and task management applications are available for both desktop and mobile devices, and include to-do lists as well as full-fledged management for research projects. Many have a collaborative focus.
These word processing programs are useful for academic writing in general, and support Japanese input well.
Language resources include dictionary and flashcard programs useful for both reference and studying Japanese.
These are mainly desktop software that organize and sync notes, and allow for the attachment of PDFs, images, and other files. Some are paid, and others are free but offer paid accounts for syncing large libraries of files.