Which computer video games can improve intelligence, barring Medal of Honor?
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