The common advice against using a "work email" is usually along the lines of "You're using company resources to find a new job, and that's (probably) not kosher according to your company's internet use policy." -- If your boss finds out (or IT finds out and rats you out), it could be very detrimental to your career.
In your case, being that it's your domain, I don't personally see a problem with it, but be aware of two things:
- Your prospective employer will judge you by the image your company's site presents.
firstname.lastname@example.org doesn't stand out. A domain they've never heard of does. Expect them to visit your site, and have a placeholder or something nice to look at.
- If your email breaks that's BAD.
If GMail, Hotmail, or a big ISP has an outage, everyone knows it's not your fault.
If your system blows up, you look bad; especially if you're applying for an IT job!
Also pay attention to AlanBarber's advice about making sure your email address looks/sounds professional. I've seen some awful things that got an express trip to the shredder...