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Edit: I think my takeaway is to primarily judge people on demonstrated knowledge rather than declared knowledge.
Edit 2: But having said that I still wouldn't draw attention to the self taught thing if I were you.
For the image aspect, I often worked with self-taughed people who lacked generic knowledge like design patterns, but where openly enthouthiastic about learning anything new. Overall it's a wash.
One can only really teach one's self to program.
List your work experience prominently and highlight your responsibilities and achievements.
You might have a slight disadvantage during the initial part of the recruitment process (resume submission). My advice in regard to that is to try and get in touch or meet the non-HR people at the company. That way you get can a referral and your resume is just a formality. If this isn't an option for you, the just make sure you keyword your work experience well, and pray. :)
I am a self-taught programmer, granted with a bit more experience than you. I have actually very seldom if ever been asked about my educational background during an interview, and hint: Those companies that made a big deal of it? I usually ended up turning down their offers, due to a very distinct lack of interest in working there that had nothing to do with them questioning my education.
The education check, if it does come up, is usually more to check for generic knowledge, algos, patterns, etc. Know these things, and know them well. Understand testing software. Understand SCM. In short, be a professional developer, and I'm pretty sure it won't be much of an issue, unless you make it one.
Relevant Experience: Worked as an engineer, senior engineer, lead developer, senior lead developer, and currently, a VP, Engineering...for companies ranging from 1-50,000+ employees. I have built and led multiple teams ranging from 2-21 developers in various mixes of on and offshore developers.
Edit: Unlike many of the commenters, I am not afraid of looking for work, and I don;t think you (or they) should be either! Its a great new adventure, I generally move within 3 years at this phase in my career, and I seldom if ever have any issue lining up interviews and competing offers, following the advice above!
Here is what you need to know: It doesn't matter. Most people are biased in one way or another. Stop trying to make other people happy.
The most important thing is that you have the skills to do the job required. In interviews, draw on your skills and past experiences to answers the interviewer's questions to the best of your ability. If that isn't enough, believe me, you don't want to work there anyways.
Most people are biased in one way or another. Maybe your interviewer is self-taught and maybe they aren't. Perhaps they've worked with a terrible engineer that was "self-taught" or maybe their self-taught engineer was the best thing since sliced bread. You can't pretend that this won't cost you a few job opportunities, but is that so bad? Ask yourself honestly, do you want to work with someone who doesn't think you're competent because you didn't go to Stanford?
Personally I prefer self taught engineers over university or other education. Autodidacts are generally more motivated to learn in my experience and represent the very best engineers I have had the pleasure of working with.
The best university educated minds I have worked with have tended to come from non-CS backgrounds, specifically mathematics and physics.
This is not to say CS degrees are not useful, just my personal anecdotal evidence leads me to favor the self taught, mostly for their attitude and general grit.
However, because ignorance is bliss, try to keep humble about your advantages over those university graduates who came to focus on other aspects of the trade. Be aware of your own value and sell what you're good at. Also, make sure that you are legally allowed to refer to yourself as an engineer. In some countries, it's a very specific title controlled by a professional organisation.
Believe me, it's much harder for a CS graduate to get a job without adequate practical experience than it is for someone with a decent portfolio.