gsdx9 v0.11.4:
http://forums.ngemu.com/717530-post1.html

gsdx10 v0.1.4:
http://forums.ngemu.com/1235303-post1.html

I've found that setting the 'internal resolution' in the gs plug-in to match what the game runs at (as reported on the window frame) gives a good speed boost.
I'm not sure yet if this is the really just the same as ticking the 'native' checkbox.

Pay attention to menus and videos running at higher resolutions than the game itself - pick the res that you see when you're in-game. Then pick a full screen mode close to that as well afterwards - running in full screen mode gives a boost as well.

S