Biology[]
Unipro UGENE is a great free program for Mac, Windows, and Linux that can do all sorts of things with sequence data. It's my go-to for analyzing the .seq and .ab1 files that are returned to you when you send things out for sequencing, and there are a few tutorials for using it on youtube and on the UGENE website.
Cytoscape, using the BiNGO plugin, is a great way to look at gene ontology group representation in gene lists.
Zim Desktop Wiki is a great free program for taking seminar notes on your laptop.
Sharing Files and Data[]
Dropbox is a program that allows you to synchronize an internet-hosted folder with any number of collaborators, on Windows, Mac, or Linux. The only catch is that you get 2GB for free and for more than that they charge.
YouSendIt is a service that will let you email a downloadable link to a file up to 100MB for free, if you need to send a large file to someone outside of Dropbox, that exceeds the recipient's email service's maximum attachment size.
7zip is great completely free software that adds great compression capabilities to Windows, so you can right click a group of files and select "add to archive" to compress them into a zip file (or whatever format you like), for easy emailing / YouSendIt / dropbox / etc. This capability is built into Linux already by default, although most distros also have a repo for 7zip (which has especially good compression ratios), and on Mac I'm not sure actually.
Free Alternatives for Everyday Software[]
These are alternatives to software you'll use all the time in lab. They're mainly handy if you find yourself somewhere without a copy of the paid versions but need to get something done, because they can be downloaded easily from the internet anywhere. They're also nice because all of their successive versions are compatible, and run on Windows, Mac, and Linux exactly the same way, which is nice if you need to explain to someone else how to do something very specific using one of these programs.
Microsoft Office - LibreOffice
Photoshop - GiMP
Illustrator - Inkscape
InDesign - Scribus
EndNote - Zotero
Prism - SofaStats can do a lot of the same things, but does not support survival curve stats. In the longer term, as a much better but not identical replacement, consider investing time in learning R.