Which "certain apps"? Watching a Flash video on Firefox sometimes disables my email notification. Do you lose sound entirely? I have a touchpad on my netbook, and if my pointer is hovering over my speaker in the taskbar, I sometimes mute it while typing. As for on the fly soundstart, alt+F2 and enter alsamixer, I think that's what does it. If not alsamixer, some other command.
I'm still on kde3.5, so I don't know what conflicts previewing in dolphin might produce.
Please be aware of the noob portion of my name. Any suggestions I have are from a sincere desire to help, but my lack of knowledge might make them ineffectual. Since no one else is jumping in, I wanted to respond, just so you don't feel stranded. Good luck. (friendly smile)