For some people, playing Magic with the same group of people on a regular basis isn't possible. Perhaps schedules conflict, or life throws a monkey wrench into your plans, or you don't have people to play with locally.
(Seriously, it happens. Elizabeth and I went to Maui last year, and we couldn't find a card shop on the island, something which has recently changed.)
So for such occasions, we have options online.
A full confession: I don't like using Magic Online. I did for a couple of years, between times when I didn't play in person or there wasn't a shop I wanted to go to. Every time I paid full price for nonexistent cards, I died a little inside. As of 6/27/12, I have 27,000+ cards that I paid for and will never have in person. It's true that my drafting skills got better, which I'm grateful for, but I paid dearly for that improvement.
I know that some people will advocate certain events as a way to 'go infinite', where you make a certain amount in winnings and trading (sometimes using bots) to allow you to have that drafting for free, but I've never had the patience or time to manage such endeavors.
That being said, playing Magic online has other advantages. You gain a far better understanding of the turn order, interactions using the stack, when abilities trigger all at once, and the intricacies of certain mechanics. For example, when casting a spell with kicker, the game always gives you the option, even if you don't have the mana.
I know there are several options for playing Magic online, but I'm going to talk about just two.
First, the official program. Magic: The Gathering Online. A program that despite several major rebuilds has a terrible UI and very non-intutitive controls. This is partly due to the complexity of the game, and partly due to the serveral different companies that Wizards hired in the past to program this game. For playing commander...I haven't used this program. I've sat in and watched some games, and that's it.
Second, I've used Cockatrice.de's program to build first drafts of EDH decks, because I like their deck editor. If you connect with other players, you can play a game. Everything is free, but it's very utlilitarian. Nothing is automatic. It plays more like an in-person game, in that you can skip things without thinking about it, and you have to communicate clearly with the table about what is happening and when.
Let's talk about the good points first.
MTGO: If you're a token player, the game automatically makes a token of the right name, color, p/t, special abilities, everything. Even if you make a token copy of something! It also automatically tracks counters, and changes to power and toughness. I have a token deck with Cathar's Crusade, and the array of dice and stones can be intimidating. The official program takes all that stress away.
Also automatic: changes in life total, shuffling your deck, and every trigger from every ability. This is both good and bad. Here's an example screenshot:
On the left side is the stack--the collection of triggers that is happening because of Blood Artist, Pawn of Ulamog, and some other effects. Every EDH game will have these moments, where one person tries to do something and a bunch of other things happen in response, and the game tracks it all for you.
In Cockatrice, the big advantage is that you don't need to own anything, everything is free! You want a $700 Imperial Seal? Done. Every card is available to you, free of charge.
This leads to the downsides of the two programs, and frankly, these are massive.
Though everything is free in Cockatrice, this means people are free to build the silliest decks around. I wish I meant silly in a fun sense, but my experience has been that the goal is to assemble as fast a set of combo wins as possible. Temple Bell/Mind Over Matter? Done. Black cards and rituals to build a huge storm count? Blah.
In the official MTGO, you have to do everything in order, without any of the shortcuts we use in live play. I have BA out as in the screenshot. Let's say three creatures of mine die--I have to choose which player each time for Blood Artist, instead of "You lose three, I gain three."
Plus, in the official game, you have to buy/open/trade for the cards in your deck. Since most of an EDH deck will not be from a current set, there's no hope that you'd ever be able to redeem your online cards for real ones.
Both programs have two major flaws:
1) Screen space. It's hard enough to keep track of the bazillion things that are going on in a Commander game in person, with a decent-sized table. If you don't have a huge monitor and great resolution, the cards get shrunk/you can only see part of the table. Neither solution is a winner.
2) Lack of personal interaction. If you have listened to the podcasts at CommanderCast then you've heard the idea of the 'social contract' that is present in EDH. I agree that the heart of a good Commander game is the interaction of the people playing the game--that's how a game lasts a couple of hours and yet everyone has a good time.
When you're playing online, there is only a small window of chatting, which is usually dominated by the running log of what is happening. At the least, I like to chime in with "Oh no" or "That's amazing" but a winkyface is the maximum of interaction for some people. That's just not fun for me.
Perhaps you'll enjoy these interactions more than I did. Maybe you'll try this and then treasure the games you play with your friends, or with other people at a big event. My goal is to make you aware of the options available to you.