What a perfect thread to necro. Fear abilities can be from special qualities or special attacks. As Soro rightly nitpicked my antimage class, they are distinct in the rules, even if players rarely have to bother with it.
The fear handbook is wrong when it says "All fear effects are mind-affecting fear effects (Rules Compendium, Pg 53)." What the RC really says is "Fear attacks can have various consequences, but all of them are mind-affecting fear effects." Only fear attacks are Mind-affecting, by the rules. Fear special qualities are not.
Frightful presence and fear auras (the two most common fear abilities) are fear attacks, and therefore mind affecting. But there could be other fear abilities that are listed as special qualities rather than attacks, and therefore be non-mind-affecting by default. Of course, they could be specifically called out as mind-affecting in their description, but all we have to do is find an example that doesn't.
Specifically, gaze attacks are out because they are attacks. Auras are specifically included. Moans/howls/shrieks are generally [M-A] anyways. It's a bit of a needle in a haystack: the first 3 monster manuals don't have any. MMIV & MMV's lack of splitting special attacks and special qualities makes digging harder an impossible mess. It is likely that WotC never thought that there could exist a non-attack fear ability/quality.
The only place this seems relevant is whether or not your DM hates your skill monkey and wants to make skills even less relevant: Intimidate. By RAW it would seem that the threat of attack is not an attack, so it is the easiest fear-based check that doesn't allow the usual "I'm immune to mind-affecting, I don't need fear immunity too" problem. It still has the usual diplomacy problems of 1) not working on the mindless, 2) requiring language in addition to 3) it can't work on the fear-immune, 4) only sets to friendly rather than helpful, 6) only works for a limited period of time after you leave, and 7) after that, sets neutrals to unfriendly or unfriendlies to hostile . But hey it doesn't eat up your swift and move action (yay?) in return for making the check's differences about the same.