I was finally able to completely circumvent this problem by enabling *both* 
indirect rendering and loose bindings for compiz (by modifying the appropriate 
line in /usr/bin/compiz). Compiz runs really fast now (a lot (!) faster than 
with indirect-rendering only and even more faster than without both).
I'm running an unsupported combination of software versions however, so could 
someone check whether this works with plain Intrepid, too?

I am running:
Ubuntu 8.04 with stock compiz 0.7.4
Nvidia driver 180.29, installed manually
on a Quadro FX 370 (dual monitor setup)

Without loose-bindings I especially had very bad performance when
running OpenGL applications with compiz enabled.

I now have in my /usr/bin/compiz:
build_args()
{
        [...]
        if check_nvidia; then
                if [ "x$INDIRECT" != "xyes" ]; then
                        COMPIZ_OPTIONS="$COMPIZ_OPTIONS --loose-binding 
--indirect-rendering "
                fi
        fi
}

-- 
Screen refresh problems with nvidia on intrepid
https://bugs.launchpad.net/bugs/269904
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