Mac OS X specific issues
How can I make the Alt key work ?

If you find yourself unable to use Inkscape functions that require the alt key (i.e. option key) such as Alt+D to create a clone or Alt+Click to select under, you will need to turn off the "Emulate three button mouse" under the Input Preferences for X11.

Recent X11/Xquartz versions (≥ 2.5.1) have a new GUI option in the preferences dialog to make the option/alt key work like a real Alt modifier instead of Mode_switch (X11 Preferences > Input > Option keys send Alt_L and Alt_R). Changing this setting will have the downside of no longer being able to input diacritic and other special characters via keyboard in X11-based applications because both option keys will be changed - see below for a more fine-grained solution.

If you still cannot get it to work you can try using a keyboard mapping file for X11 (the environment Inkscape is running in) called an xmodmap (keyboard modifier map and keymap table). Open a terminal and type

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cd ~
touch .Xmodmap

This will create a new text file called ".Xmodmap" in your home directory. The period before the actual file name "Xmodmap" causes the file to stay hidden within the Finder.
Now open the file by typing

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open .Xmodmap

and paste the following into the newly created file:

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keycode 66 = Alt_L

This defines the left option key as alt within all X11 applications, enabling Alt based shortcuts. You need to re-start X11 to see the change.
The right option key stays the same though, so you cannot use it as Alt but you can still use it to type special characters such as é, ß or \ on non-US keyboards (which is Shift+Option+7 on a German keyboard for example). It makes typing those letters more cumbersome but the user (unfortunately) has to determine him/herself which of the two functionalities is needed most for his/her daily business.

How can I make keyboard shortcuts work with Command instead of Control ?

Inkscape runs under X11 and is originally a Linux app, so all keyboard shortcuts are based on Control and not Command as in OS X. For example, Copy is ⌃C and not ⌘C. You can use an ".Xmodmap" file to switch the behaviours of Control and Command in X11 applications. See above how to create and open the .Xmodmap file. Then paste this inside:

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! Switch meta and control
keycode 67 = Meta_L
keycode 63 = Control_L
keycode 71 = Control_R
clear mod2
clear control
add mod2 = Meta_L
add control = Control_L Control_R

Finally, in X11, make sure that the option "Enable key equivalents in X11" is unchecked and restart X11. Now ⌘C should copy, ⌘V paste etc.