Apple - Restricting Command+tab options to only apps that are in the current space
control+F4. Cycles through the applications in that Space.
(I actually have this mapped to control+`; which I find easier to remember, being close to the cmd+`; to cycle through an application's windows.)
To change the keyboard shortcut, go to the Keyboard preferences, Keyboard Shortcuts, and Keyboard & Text Input. It's the 'Move focus to active or next window' option.
(Edit to fix the keyboard shortcuts; I didn't realise that the backtick character wasn't showing up.)
Yosemite
This behavior can be mapped to your desired key combination like so:
System Preferences > Keyboard > Shortcuts > Keyboard > Move focus to active or next window
Mavericks
^F4
does switch through windows in the current space but you may have to upgrade to Yosemite to map this behavior to ^~
.
But the problem can still be alleviated like so:
System Preferences > Mission Control > Uncheck "When switching to an application, switch to a Space with open windows for the application"
I know Hyperswitch didn't exist when that question was asked, but it is a modern answer to that question, and it is much better than hacking with Karabiner (formerly KeyRemap4MacBook) and/or struggling with the system preferences (since they don't accept any key mapping for every command).
Please see https://apple.stackexchange.com/a/127414 and upvote it if you find HyperSwitch useful.