Compiz and desktop shortcuts

One slightly annoying thing about Compiz is that it grabs control of some global shortcuts - I heavily depend on Katapult (default Alt+Space), the run dialog (Alt+F2) and the occasional XKill (Strg+Alt+Esc).
Fix:
1) Go to CCSM->General Options->Commands tab
2) Under "Commands", you can define up to 12 entries.

Katapult:	katapult
Run dialog:	dcop kdesktop KDesktopIface popupExecuteCommand
XKill:	xkill

3) Associate any keyboard shortcuts you want under "Key bindings". If there is a conflict, compiz will notify you. Compiz had already set Run dialog for Alt+F2 before, but for some reason the shortcut didn't work this time. Also shortcuts containing Esc will not work, you have to choose a different one for XKill.

Global shortcut conflicts (Amarok example, most KDE programs work analogously):
Amarok shortcuts seem to be generally window-manager-independent, however, conflicts are resolved in favour of compiz. This usually affects Win (Super) + C (Enhanced Zoom/Group and Tab Windows) and Win + Z (Put Windows).
The easiest way is to change your Amarok shortcuts: Amarok->Settings->Configure Global Shortcuts…
If you want to keep the Amarok shortcuts and to know exactly which compiz plugin is blocking your shortcut, do a grep (found here) in /etc/gconf/schemas:
grep -A 2 '<Super>c' /etc/gconf/schemas/*.schemas
(XML file, so use HTML string notation. Example for <Super>C, adapt if necessary). Either change the shortcut directly in the affected .schemas file (check whether the plugin is active), or use the CCSM GUI.

KDE 4
Global shortcuts are managed in the Personal Settings manager (Keyboard & Mouse) for all KDE4 applications.