There are a couple of apps one can use. The most popular are commercial and semi-commercial "VTT" applications (Virtual Table Top). Typically they have features for maps, character sheets, even combat trackers, etc. as well as, of course, chat and whisper, but usually not voice chat. Some examples include:
Fantasy Grounds (Commercial--Mostly designed for D&D, but they have fan supported rulesets for Shadowrun)
OpenRPG (Open Source out of development now, but as far as I know still functional. XML/embedded html based with lots of fan resources on the web)
Battlegrounds (Better suited for table top boardgames and maps VTT, but theoretically designed for RPGs as well. In some sort of shareware state)
Vassal (Truely built for wargames, but fans have built RPG modules for it, but not afaik for Shadowrun)
And there are older VTTs as well. Most of these can be used in combination with Skype, Ventrilo or Teamspeak should folks be so inclined, but it is uncommon.
There are also some other options. A lot of people use text-based multi-user games (MUSHes) to run online games. There are a few MUSHes specifically designed to act as gaming servers, with special infrastructure built within the game's internal scripting engine to support common gaming actions. Some people also like to run games on IRC with a die rolling bot and sometimes mixed with one of the voice apps above. Someone else on this forums is running a game using GoogleWave, which sounds very cool to me

, particularly with some extensions.
There are undoubtedly other options I'm not recalling at the moment. The real challenge in my experience is finding enough people willing to use any particular medium to play SR.