appear.in — Browser-based video conferencing.
BlueJeans Conferencing — Video-conferencing and screen-sharing — works well with faulty connections.
CardBoard — Story-mapping and shared card analysis.
Invision — Prototyping, collaboration & workflow platform.
RealtimeBoard — Online whiteboard & online collaboration tool.
Red Pen — Fast deliverable feedback.
VSee Messenger — Low-bandwidth video conferencing.
Gliffy — Collaborative diagrams — flow charts, log frames, etc.
Skype — Cross-platform messaging, able to use an account (with money added) to send/receive calls from traditional phone lines. Available on iOS, Android, Blackberry, and Windows Phone.
WhatsApp — Cross-platform mobile messaging app which allows you to exchange messages without having to pay for SMS.
Adium (MacOS) — Chat client for MacOS systems that supports AIM, Bonjour, Google Talk, ICQ, IRC, Yahoo!, and others.
EtherPad — Customizable online editor providing collaborative editing in really real-time.
Pidgin (Windows) — Chat client for PCs that supports AIM, Bonjour, Google Talk, ICQ, IRC, Yahoo!, and others.