I have been running an online Shadowrun game since last year when the PDF was released. My players are scattered around the country. Myself and a friend are in Vegas, and we have players in Florida, Eastern Canada, and Cyprus. So, online is a must.
We use Skype for the voice
we use
http://rolz.org/group# for the dice roller. It has codes you can use to count Hits, and reroll 6's if you use Edge
We use
http://rpgtableonline.com/welcome.php For the game table, where I can draw maps when I need to. It is mainly formatted for D&D, but it's easy enough to work around. The dice rollers aren't so easy to work around, which is why we use the roller above. It has it's own voice client, but it gives some people trouble.
So, I've been running a game for nearly a year there, every other week, and have had pretty good results. Most of my players were formerly non-Shadowrun players, but they've gotten pretty interested now, looking out for new books and the like.