Kevin, fantastic topic - over the years it's been a real annoyance to me so it's great to find someone that thinks and acts the same way I do! I had begun to think I was unusual in showing respect by paying attention to the person no matter what the topic of conversation.
When I'm on instant messenger I always pay exclusive attention to the person and I get very annoyed when I know from the pauses they aren't doing the same to me - I just treat it like if I were stood in front of them, in which case, it would be seen as extremely rude if they kept interrrupting our conversation to have simultaneous conversations with other people at the same time. I rarely have more than one conversation going at once, and if I do get several I warn them and try to close out all but the most involved.
For me, it's a simple issue of respect, or lack thereof. It's ironic that the people who do the most ignoring/multitasking are usually very self-centered and would get upset if they were being ignored or not treated seriously when they wanted to talk.
If the topic is something I'm not interested in, or don't want to talk about, I simply say so. I don't let the person believe I'm interested and paying attention unless I really am - again, that's simply a lack of respect.
As you said you look out for clues that inconsequential things have been noted. I pay particular attention to that myself, both in demonstrating to others by things I say, ask, or do and by looking out for the same signs from them. In fact, I use this as a basis for deciding if someone is worth becoming close friends with.