The workaround linked by manatlan is working but forces usb1 speed.

It seems that also adding the "acpi=force irqpoll" boot option (as
described here: http://www.ubuntugeek.com/how-to-fix-usb-stops-working-
problem-in-ubuntu.html ) improves things a bit: it just revived my usb2
connectivity and seems to keep it working for now.

Could it be usb controller related (i.e. Intel ICH8)?
problematic ones on my system are
00:1a.7 USB Controller: Intel Corporation 82801H (ICH8 Family) USB2 EHCI 
Controller #2 (rev 02)
00:1d.7 USB Controller: Intel Corporation 82801H (ICH8 Family) USB2 EHCI 
Controller #1 (rev 02)

While on an older system the ICH6 is working just fine
00:1d.7 USB Controller: Intel Corporation 82801FB/FBM/FR/FW/FRW (ICH6 Family) 
USB2 EHCI Controller (rev 04)

-- 
device descriptor read/64, error -110
https://bugs.launchpad.net/bugs/433438
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