We much preferred VSee to other chat programs and play-by-post or -e-mail gaming. As far as dice goes, you can't go wrong with dicelog.
The most difficult challenges was keeping people focused, from a DM perspective. Being at the same table contributes a lot. I combated this by preparing many, many speeches and such in advance, as well as working toward roleplay immersion as best as I could.
Also, finding a program to use maps easily with. Using VSee, I turned Excel/Calc into an easy dungeon model for combat. If you can, use RP Tools Maptools, I've heard it works beautifully but I haven't had the time, energy or patience to sit down and learn the system (it appears to be labor intensive as far as setup goes). Should that go well for you, please share your experience with those less smiled upon by the programming gods.
The best aspect was the time constraint lift as simply arranging a time to be online was enough, as opposed to waiting for people to arrive and allotting time for people to depart. That, and not having to hide all my papers behind a screen. Me being in front of the computer (where my backup PDFs are as well as the d20SRD) was more than acceptable, it was required.
The last part having been said, one of the worst aspects is your roleplaying is only as wide as your webcam/microphone can view/hear, and the fact that we human mortals are not designed to be in front of a desktop for incredibly long times with no reprieve. Walking away means walking away from your players, so recess is a lot less fun than when everyone's in the same room as I see it (I work extra hard on prep so I get recess as well when with the tabletop group).
Plenty of my sessions have gone long enough, as DM I could call it at six hours. I had the advantage of dedicated gamers, however - they had a lot of time slotted. The rest is all up to one's PC and internet connection, as well as those of everyone involved.