For a little under a year now, I have been using RPGTO to run an online shadowrun game. The table doesn't handle success based rolls well, so we quickly switched to rolz.org for rolling. RPGTO is formatted for d&d4e, but with their drawing tool, and a little creativity, it is devent enough to draw out maps for use with SR. It has tabs for Player and GM notes, so that is nice too, as I have been able to enter information and track the events of my campaign.
Recently we discovered that roll20 has SR5 character sheets available now, and since it does handle success based rolls, we decided to check it out. I just finished running my first game with it tonight. Skype's voice is better, as the table voice seemed to let in a lot more background noise, so we disabled table voice, and used skype for the voice.
If you download RPtools, or specifically tokentool, then you can pretty much make tokens out of any image you can find on the web. I found a way to assign some of their status bars to physical and stun damage tracks, so that seems helpful. Right now, we are trying to figure out if there is an easy to way migrate tokens from one map to the next, because right now I had to assign all the values individually, on each map we used the tokens on, and that just seems a little convoluted.
roll20 does not have the same convenient journals for player and GM notes, so you need to come up with your own system for that. But, it does allow for the ability to take screen shots of maps from SR products, drop them into roll20, and if they happen to have grids, you can easily resize them to the grid on the table, though some of the scales look weird when you actually get to the scale with the grid.
Other than that, I think we are going to give roll20 another try, and may migrate to it permanently.