Is it possible to add shortcut key for the commands like 'Refresh from Server' as shown below (in Eclipse aka force.com IDE)?
Note: I tried going to Preferences => General => Keys .. doesn't work.
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I looked into this a while ago and found that it is not possible. The implementation of the Force.com IDE plugin doesn't use commands which is what you'd need to be able to set up a keybinding. You can get a peek into the implementation if you unzip the eclipse/plugins/com.salesforce.ide.ui_184.108.40.206302151147.jar (possibly a different version number for you) file and look at the plugin.xml file. Alternatively you can use the Plugin Spy functionality of eclipse to get more information.
You could look into using a more generic eclipse macro plugin and see if that works.