My main 3.X campaigns have all been online, over basic IRC (we started over 5 years ago before most of these tools were even under development). When we use grids, I tell everybody how big it is, and we use the number/letter thing to do it (Knight to H4!). But for the last several years, we rarely bother with a grid in combat; we use what amounts to an honor system. The players trust me to keep track of where everything is, and ask questions like "How many can I catch in this fireball? Can I get all six?" I happen to have a good head for spatial reasoning, so for me it's easy to track everything mentally- others might find it difficult, but then again a DM can always use a battlemat on his/her own side to track stuff.
Communications happen by using basic quotes "" for any words spoken by the characters, () for any out-of-character comments (often coupled or prefaced with an OOC), the usual /me command to denote in-character actions (players always change their nick to match the character name, to make this work), ## to enclose any telepathy (happens a
LOT in my games due to the presence of PC illithids among other things), and finally the tildes ~~ are used by me to denote any special mode of communication that doesn't fall into the other categories. An example of the latter is that when an Uvuudaum "speaks" in my game, it's described for flavor purposes as the thousands of mental voices making up the cacaphonic mental "noise" that constantly surrounds the creature (thus explaining its
Confusion aura among other things) suddenly synching up and thinking the same thought all together, and then inexplicably doing it again and again to form a complete sentence. One can't really use the normal telepathy marks for something like that.
Good luck with your online game- having done both online and offline, I can honestly say that there are many advantages to doing a game online that can help make up for the disadvantages. I'll expound on my two favorite ones below.
The biggest advantage by far, IMO, is logging- running the game in IRC means you can set your chat client to log the chat, and thus save a complete record of everything that happened in a game session without any effort- even the OOC comments and timestamps to show delays if that's important for some reason. There is thus no arguing about what happened last session, or what exactly was said to launch the characters on their current quest, or the like- because you can just go into the old logs, find the appropriate text, and cut'n'paste. It also helps get players back into the mood of the game, because the DM can copy a partial chat log of the last game to remind everybody of what was going on- sort of a "Previously, on D&D Game" episode opener. I really don't know what I'd do without my game logs- the next time I run a face-to-face game I'm certainly going to miss it, perhaps enough to come up with an alternative.
The ability to start up subchats with other people in the channel is another big plus for RPGs- no more worrying about the effect of passing secret notes around the table. Yes, I know one can pass blank notes for psychological effect, but let's face it- it's a lot more interesting if nobody who isn't in on the secret even has an inkling that there's a secret to know about, isn't it?
Of course, players are perfectly capable of passing secret notes between themselves behind the DM's back this way, but on the whole if your player group has built a trust this shouldn't be a problem. It also helps when you have to "take a player aside" to describe something that happens only to that character, like the destination of a one-time teleport trap or the fact that a doppelganger just cold-cocked him and took his place.