Here are the reasons I see as to why anyone would want an alternate account:
1. To confuse people. Sometimes works, sometimes doesn't, depends on if you wanna really confuse them or not.
2. I suppose some staff may use them so they don't have to worry about their positions all the time. I mean, they'll still do their job, but sometimes they may not want to be bugged by n00bs and whatnot all the time. Some users may do this too, I guess, especially if they own something very popular, like a successful hack or graphics shop.
3. Before name changes ceased to exist, they were there as placeholders, so when the time came for your name to be changed, you wouldn't have to worry about your desired name being taken.
4. People have turned alts. into RP accounts. It's kind of like a "Muse" or "Puppet" on LiveJournal--their username usually represents the character, and their posts reflect their character. The only exception is, of course, you don't get 15+ icons to choose from whenever posting, unless you post an image in every one of your posts. But if you don't have 15+ posts that count, then that's impossible to do.
I follow numbers 1 and 3 mostly. Although, with 3, it's because if I like a certain character/series/etc., I'd like to have an account of that, not just because I want a placeholder.