How many minifigs have actually flown in space?
Actual Minifigures In Space
There have been a number of videos posted from the ISS mission, where we can clearly see one of the astronauts (Satoshi Furukawa) on the station holding a model with some minifigures:

On the Gallery Pages they list out &quot;Working and living in space - This is the LEGO models shown in the videos&quot;
In the shots there are there are at least 7, if not 8 minifigs (assuming that each hair and face is part of a complete minifig, rather than having the bodies reused for the shots):






This appears to be the first time actual articulated minifigs have officially gone to space.
A Romanian named Oaida Raul sent the Lego Shuttle [bs:3367] up on a weather balloon to &quot;the edge of space&quot; on 31 December 2011, but hasn't released actual figures of the altitude reached:

2001: A Brick Odyssey


Two Canadian Students sent a Minifigure up to the stratosphere in January 2012, high enough to see the curvature of the earth, which can be seen reported on the Toronto Star's pages:

Minifigure Statues
Before then the closest thing to a minifig officially sent to space are the three custom built aluminium Minifigure statues that went up on the JUNO space craft this year:

JUNO Spacecraft to Carry Three Figurines to Jupiter Orbit


The Roman god Jupiter, his wife Juno and Galileo Galilei
This wired article concludes:

This unique project has put a smile on many Nasa and Lego employees' faces and stirred up interest from other state space agencies, as well. Will LEGO minifigs take another trip in space soon? Time will tell. But until that day, keep an eye on the sky for the fastest moving toys in the universe.

LEGOSpace.com's insistence on not supporting deep-linking fails me, but if you go to the Education Blog and scroll to Thursday, August 04, 2011

LEGO® Minifigures on a mission to promote space research
Three LEGO® Minifigures leave earth on the Juno deep-space probe today on a five-year mission to Jupiter to broaden awareness of the importance of planetary research.

Pictures of Minifigures
Prior to these two missions, previous missions have been promoted as sending Minifigures to space when in fact what they actually contained were pictures of minifigures:

LEGO bricks and products have been on several space missions. The latest mission with NASA was in 2004 when two astronaut minifigures hitched a ride on the Spirit and  Opportunity Mars Exploration Rovers.

When in reality what happened was:

Today, Opportunity returned pictures from Mars of another three “LEGO Bricks” and Sandy Moondust, the second “astrobot” representation of a LEGO Minifigure.