Thanx for your replies, but I already know the problem comes up during a disk write, no need for iostat. And it is not general slowness I'm complaining about, everything runs fine except for the few minutes every morning.
I don't think it is a hardware issue, because I have another computer with completey different hardware that does the same thing. So it must be an LMDE or Wheezy specific configuration issue. Or maybe a Mozilla issue, because it happens only in Iceweasel and Icedove, but I can use other applications.
Some process is creating havoc for a few minutes, but I can't pinpoint the problem because there is nothing in the logs at the time of the disk write
I'll try running Chromium for a day and see if the problem arises. And I'll check with atop.