Thanks for all the answers. Of course my computer is an apple computer, a really nice powerbook g4. with 10.4.7 installed. The ? over the apps is not over the icons in the dock. It's over all the apps in /applications folder. I have discovered that they stay like that for some time (some restarts) and then they are gone to be back later (don't know yet why they come back). I've been thinking if I had installed or done something to comprimise the system, but it's been a while I have kept my computer untouched (no new installs, only work with documents)
I wish I didn't had to reinstall !!!