This got me to thinking about why I did not feel right about sending a condolence note through email. It would have been easier and quicker, after all -- which I think is part of the reason why it seemed wrong. Part of what you are looking for is a way to indicate, in some fashion, how much the person to whom you are writing (and his or her welfare) means to you. Efficiency seems not only beside the point, but counter to the point. There's also, oddly enough, the matter of handwriting: You most likely see all your email in the same typeface, no matter who wrote it. But penmanship is distinctive. Whether the distinctive associations we have with an individual's penmanship remain now that we mostly don't send letters through the mail any longer is questionable, though.
I've had cause to think about this issue again recently, and I'm not entirely sure how I feel any longer. Has electronic mail replaced hard-copy mail in terms of its cultural meaning and use? I know that at the core it matters far more that you send a note than what medium you send it through, but I still think that formats and protocols have resonance. On the other hand, I now find myself in a situation where a condolence note sent through the mail will likely arrive after various other online encounters. You want to say, "First off, I'm so sorry for your loss. Now, about what you just wrote in that forum..." That doesn't seem to be an answer either.
For now I'll stick to the handwritten note.
I do know how I feel about a variant of this issue: Offering condolences in a public online forum. In some ways, I don't understand this. Offering condolences is a good thing and, as I note, the most important thing whatever the medium. But were I to write a note like this to a public forum it would feel to me as if I were saying, "Look everybody, I'm sending my condolences." It would feel as if I were parading my piety. If the audience for the note is the mourner, why send the note to anybody else? I know, I know, I know -- self-promotion is not in any way the intention of these notes (with only one exception I can think of in my experience), and in fact I've read some truly lovely notes of this sort that have been written publicly like this. Public rituals of grieving or of remembrance and support are definitely something I think is good and important -- but those are specifically group and community things, not personal condolence notes. In public forums these two things get confused. To my sense of personal protocol and what I myself feel comfortable with, "I'm so sorry for your loss" belongs in a one-on-one encounter.
These things evolve, I think.