Academic

• Anki - Anki has completely changed the way I study by making it extremely efficient and easy. The gist of it is that you make flashcards based upon course content (e.g. lecture slides, textbook, etc.), and using their algorithm based on spaced repetition, Anki shows you content when you're likely to forget it. I like it so much, I made my own video about how to use it. I also recommend the book Learning Medicine: An Evidence-Based Guide. The eBook is the best $15 you can spend to equip yourself for success in any class which is memorization-focused (read: life science classes and psychology classes). Note that there are other apps out there using the Anki name. Don't use them; the learning curve for this version is well worth the time investment. 
• The Pomodoro Technique - Sitting and focusing for long periods of time is tough. Taking scheduled breaks helps make any task better, and I have found the Pomodoro technique stellar when making flashcards for lots of lecture content. I use Tomato One for macOS, but TomatoTimer is just as useful. Make sure to turn on notifications in your browser!
• Notability - A document annotation and note app for macOS and iOS, Notability has made marking up lecture slides a breeze. I download the lecture slides from our eLearning portal, save them as a PDF, then import them into Notability. Don't waste paper printing out slides anymore. I have it set to sync via iCloud, and to back up the annotated documents to my OneDrive account, and I export the notes at the end of each term to hard drive. It now features searchable handwriting. Especially great with iPad (2018), any iPad Pro model, and, importantly, Apple Pencil. (Note: they seem to be moving to a subscription model. It is arguably still worth the money)
• Mendeley - I recall high school where we would use EasyBib to generate citations for our essays and lab reports. It was fine then, but university demands a more powerful tool. Mendeley allows you to import citations from papers and books (via Google Books) to their app, and to automatically generate and insert the citations into Microsoft Word. It too takes some time investment, but I found it to be well worth the time I spent learning it. You may have to manually clean up citations in APA format; check with your professor or TA that the citations Mendeley generated for your assignment are acceptable. 
• Unpaywall - Google Chrome and Firefox extension that checks if a copy of the paper you're looking at is available for free (e.g. if an author uploaded it to their website, or if it is uploaded to the institution's website), and if so will present a link for you to download it. They claim to have links for about half of all total papers.
• EZProxy Redirect - many universities host a proxy for students to log in through to access articles, but if you've come across a closed-access article that you want to access, it can be a pain to try and find it through your school library website. EZProxy Redirect is a Google Chrome extension that will pass the link through your school's proxy, so you can access it easily. It has support for tonnes of schools, and is free!
• Taguette - there has been a dearth of free, open source qualitative software for many years, only now being filled by this wonderful tool. It runs as a server on your computer and it can be accessed through a web browser and has most of the foundational qualitative analysis functions one would expect (coding, hierarchical codes) are present. Of note, I find the export options to be particular exceptional, including as .docx and .xlsx files.

Administrative

• Mail.app or Microsoft Outlook - Most institutions are moving towards either Google's GSuite or Microsoft's Office 365 for email. Both are great for different reasons, but I really think they shine when combined with a dedicated desktop email client. The power of having all of your messages available offline, easily and quickly searched, and with convenient notifications is in my opinion unbeatable. There is a reason most organizations use either the built in Mail app (on macOS) or Outlook (both macOS and Windows, as well as mobile, where it is particularly recommended): they are best in class. 
• Ferdi - In the last few years, a large number of these omni-messengers  which aggregate a bunch of messaging webapps into one. While none of them are perfect (there's always some little issue, like notifications not coming through, or services needing to reload), I've found Ferdi to be a great balance between features, ease of use and broad service coverage. 
• Google Drive - You probably know about Google Drive, but I would be remiss to not mention it. Drive provides 15 GB for free and is an amazing way to store a lot of files. Native G Suite files (e.g. Docs, Sheets, Slides) do not contribute to this limit. I really like using Sheets to collaborate on scheduling events and organizing information with others. 
• Diagrams.net - Making quick diagrams to explain a process or layout is doable in PowerPoint (although Microsoft has the very expensive Visio for this purpose), but I believe that dedicated software is better. I prefer Diagrams.net, as it is a free, fully-featured, webapp which makes very crisp and professional looking diagrams. It also integrates nicely with Google Drive, giving you a great place to store them as well. Especially good for diagramming the flow/steps of an experiment. 
• Miro - Brainstorming remotely or digitally can be challenging, as many platforms lack the fluidity and flexibility of using a whiteboard or sticky notes in person. I think Miro comes close, and has an extremely generous student plan. It also has a large number of powerful templates built in, and I think is a great fit when trying to work remotely. The student plan also has a sharing feature similar to Google Drive, where anyone given a link can edit the whiteboard.
• Trello - A surprising amount of academia is project management. I like Trello for its featureful free plan, which allows you to visually separate and organize projects to ensure you are on top of all aspects of it. Collaboration is also free in Trello, making it particularly useful for team use. 
• Microsoft OneNote - In the spirit of the administrative nature of academia, I like using OneNote to organize all of my meeting notes. This is one of its primary functions, and it works wonderfully for this purpose. I of course use the rest of Microsoft Office as well, but I find that folks often don't know what OneNote does. OneNote is also totally cross-platform.
• Microsoft Office Lens - Of the many scanning apps available for mobile devices, I find Microsoft Office Lens (iOS, Android) produces the best images. It can also save the resulting scans as images, PDFs, or directly into OneNote. Totally free!
• Reminders.app - the default Reminders app on iOS is great for one single reason. You can yell out "Hey Siri! Remind me to do x at x o'clock", and she will faithfully note this and then ping you at the appropriate time on whatever Apple devices you own. I have found this especially helpful when running from meeting to meeting. Also works with calendar appointments, but I find that this isn't as intuitive.
• Voice In Voice Typing - I have been trying to use dictation for more work where precision and clarity may be a bit less important. While macOS includes a dictation feature, I have never found it to be as smoothly integrated as I would like, often stuttering in some apps. Inversely, I have found this Chrome extension to be very effective for dictation (even when speaking rather quickly), and has some tools built in to capture text for pasting in for websites that may be less compatible. 
• TinyWow - I've kept seeing this site mentioned online, which allows one to manipulate many types of files right from one's browser. A nice one-stop shop. 

Communication

• PowerPoint Templates from Microsoft - Many people don't know this, but Microsoft themselves publishes hundreds of templates for all types of presentations. Consider them.
• Showeet PowerPoint Templates - There are some amazing templates on this site, including a free downloadable SmartArt graphics collection. I think everyone communicating complex info should have that collection downloaded and available for reference: I've found just the right diagram to express my thinking numerous times in this collection. They also have some attractive slide design templates on their website, too!
• Poster Presentation Templates for PowerPoint - When I had to make my first poster presentation, I asked an upper year student where to start. They led me to PowerPoint, but I'm upset I didn't find this site sooner. Super easy-to-use templates to make sharp looking posters. Make sure to double check the size requirements for the conference you're presenting at and download the correctly-sized template. 
• Genigraphics PowerPoint Research Templates - Same idea as above, with some different designs/layouts. I would recommend checking out both sites before deciding on a template. 
• Library of Science & Medical Illustrations - This gallery of illustrations spans the health and life sciences, and can be used in just about every field in those disciplines. They can be "bought" for zero dollars: just enter a "0" at the checkout screen, but if you are able, the designers would appreciate anything you would be able to pay for them. 
• Notion - For many academics, making a website to share work or ideas can be challenging. Notion can be used to make a quick website to share with conference attendees (example) or stakeholders to provide additional context for your work. It has a great free student plan.
• Design for Scientists - An Instagram account with a bunch of tips on how to design posters and slides well! They also have a free eBook for download, which I think is worth most students' time.
• BioRender - Have you ever wondered how they make those gorgeous diagrams in papers and textbooks? They likely have biomedical illustrators on staff, but this webapp is the second best thing. The power of this software is staggering, and you can make some gorgeous, complex diagrams. With the free version, there's a watermark, but if you make your diagram in the corner opposite it, and take a zoomed-in screenshot, it'll look fine for most assignments and presentations at the undergrad level. Remember that you need to pay for the service to use diagrams you create for publication.

Photos and Icons

• Pixabay
• Needpix 
• Unsplash
• Pexels 
• Shopify Burst 
• Barnimages
• Flickr - Make sure to adjust the license in the dropdown when searching so you don't run afoul of copyright
• Morguefile
• Vecteezy
• Pictography
• unDraw - Images can be downloaded as SVGs and PNGs, and can be recoloured on the website!  At the time of writing, these images can be used on commercial or personal projects with no limitations.
• Disabled And Here Collection - Disabled And Here is a disability-led stock image and interview series celebrating disabled Black, Indigenous, people of colour (BIPOC); the images are available for use under a CC BY 4.0 license, with attribution required.
• Open Peeps - a collection of hand-drawn cartoon people, with a high degree of customizability. The creator has said an online tool to customize them is in the works.

• Flaticon 
• Iconfinder
• Noun Project

• CleanPNG (note: the website claims fair use/public domain/user submitted, not that the site explicitly has permission to host the images)

Misc.

• Human Metabolism
• Biochemical Pharmacology