I see my queen in most inspections, but if I see small uncapped brood (it is very difficult for my eyes to see eggs) then I don't keep the hive open just to look for her. I am pretty good at figuring out where she is likely to be. Based on the previous inspections of the hive I have a pretty good idea if she is in the top box or the bottom box.
I have almost always found her in the middle 2 or 4 frames, so I pull a middle frame first and inspect it. If it is full of capped brood then she is less likely to be there, but if there is room for her to lay then more likely.
If she is not on the first frame then I keep it out of the hive and pull then pull the one that is the next closest to the wall (in an 8 frame box I pull #5 and keep it out, then #6 and replace it, then #4 and then #3). This way the box is divided in 1/2 and she is less likely to cross the space where the frames are missing. If I don't find her on the frames on the right side then I check the frames on the left side.
Like the others have said, I don't look at individual bees, I watch the general movement on the frame. The queen moves differently than the other bees. She moves more deliberately. She goes where she wants and she doesn't let anything get in her way. The other bees seem to move randomly, rather helter skelter. Her body almost looks like a new born baby's little finger being dragged across the frame. My queens tend to be chestnut colored and the workers are yellow and black striped, so that and her movement helps her to pop out on the frame.
Lastly, that shiny golden crown that she wears tends to set her apart a bit.