Which computer video games can improve intelligence, barring Medal of Honor? Source: Intelligence and How to Get It: Why Schools and Cultures Count (2009). p. 49.


    We have every reason to believe that these sorts of visual exercises actually improve fluid-intelligence skills and the executive functions that underlie them, including working memory and control of attention. Researchers have shown, for example, that video-game players can attend to more things at once than can nonplayers. Video-game players can also ignore irrelevant stimuli more effectively than nonplayers and can see objects in a broader visual field than nonplayers. To make sure that what they have observed of computer-game players is not just a self-selection effect (with the fluid IQ hotshots being the ones most likely to play computer games in the first place), the researchers had non- players learn a game—Medal of Honor [emboldening mine]—that they thought would teach the attention-control skills of their video-game players, and had other nonplayers play a computer game that the researchers did not believe would be capable of teaching attention control, namely, Tetris. Subjects played the computer games for an hour a day for ten days. At the end of the period, Medal of Honor players did better on the attention-control tasks than did Tetris players. 


Exclude Medal of Honor that's already cited overhead.
This paper by Shams, Foussias, et al. (2015) gives a good meta-analysis of studies that have been conducted on the effects of video games on intelligence. Some games described as improving cognition were:

Super Mario 64:


  "Significant increase in gray matter volume in the right HC, right DLPFC, and bilateral cerebellum in the video game group compared to the control group"


Tetris:


  "Puzzle game group improved in attention and visuo-spatial ability"


Starcraft and The Sims 2 (female subjects):


  "Games that emphasize rapid switching between multiple information sources led to a significant increase in cognitive flexibility"


There's many other games covered in this paper, displaying a variety of cognitive and neuroanomatical changes in subjects who played them regularly for a somewhat extended period of time (typically 1-2 months).

Additionally:


  "A number of structural imaging studies have found that video game play can alter brain structure, especially gray matter volume. These studies have typically analyzed a particular video game or video game type. The most commonly studied category in the last few years has been complex strategy games such as Super Mario 64 or Space Fortress..." (emphasis added by me)


Reference: 

Shams, T. A., Foussias, G., Zawadzki, J. A., Marshe, V. S., Siddiqui, I., Müller, D. J., &amp; Wong, A. H. (2015). The Effects of Video Games on Cognition and Brain Structure: Potential Implications for Neuropsychiatric Disorders. Current Psychiatry Reports, 17(9). doi:10.1007/s11920-015-0609-6