Calendar sharing: Google calendar
Teleconferences: Skype, Hangouts/ Hangouts on Air, with collaborative note-taking in real-time editors
Writing documents: Google docs (possibly synced with GitHub 
and including R code), wikis, etherpads, Overleaf, (Tahi?)
Software: GitHub, IPython notebooks
Collections of thoughts/ ideas/ concepts: blogs (including Twitter), Federated wiki, ThinkLab or classical document-centric software as above
Issue tracking: GitHub, Phabricator, (Trello)
Literature: Zotero, (Mendeley, Papers,) BibTeX
Presentations: beamer, wikis, Prezi, reveal.js, SlideWiki, Google slides, ...