I've noticed that the posters who are saying that they've never experienced problems or different service when dining alone have mentioned being on business trips. I think this makes a difference. Hotel restaurants, or restaurants that cater to business people on trips, are likely to be more welcoming of single diners, because more of their client base consists of people who dine by themselves. A restaurant that's not in that business doesn't necessarily think of single diners as being part of their desired clients.
I had the experience of being treated differently due to being single just last night. I went to a seafood chain restaurant (I love salmon, and being in the Midwest, a non chain fish restaurant can get pricey!). I was told it would be 10-15 minutes. 30 minutes later, after at least three other parties who came after me were seated, I was led to a 4-top, so obviously they weren't waiting for the perfect 2-top to open up. I could hear and see my server visiting all of her tables, except me. I waited for at least five minutes for her to even come over to my table. It then took her about 10 minutes to come back with my lemonade and take my order! From what I could tell, she had about four/five other tables, and probably spent two to three times longer at those tables than she did with me. At the end of my meal, she tried to give me my bill without asking if I wanted dessert, which I did want, and was visibly irritated with me when I told her that. Everyone else got a smile and a happy tone of voice when they gave orders. I got a huuuuge sigh and "Well, I'll have to rerun this, you know". It doesn't take much brainwork to conclude that I wasn't as welcome in her section because I was a single.