Off the top of my head:
A clipboard manager – Can’t do all the upcoming code copying/pasting without one!
A screen capture tool – One that allows for quick, easy annotation like Skitch.
IPython – An interactive, web-based notebook that allows “recording” and execution of command line (as well as a plethora of other programs like Python and R) programs.
NCBI Standalone BLAST – Used for comparing unknown sequences (nucleotide, proteins) with known sequences.
Dropbox – Synced, cloud-based file storage and sharing. This will be interesting because I already have Dropbox installed on my Windows partition and I don’t want duplicates of all my files. Will try to link the Ubuntu Dropbox installation to the Windows Dropbox folder. Will cover this in a separate post.