Best prog rock flautist, besides Ian Anderson.

Mauro Pagani of PFM. That man was insane genius! 

^That's a great list.

I would like to add some people which are not usually associated with flute, but when doing it, they're surprisingly good at that: Florian Schneider of  Kraftwerk and Grace Slick of Jefferson Airplane.

I won't even start with a plethora of flutists in jazz-rock...

Didier Mahlerbe (Gong)

Not one of the best, but just thought I would mention Andy Latimer too. 

Andy Latimer of Camel, Thijs van Leer of Focus, Didier Malherbe of Gong, they're all fantastic flautists, but really, in my opinion, nobody beats Nigel Pegrum!

Thijs Van Leer is personally, by contrubting his flute with very different styles like "Hocus Pocus" and classical use like "House of the King". 

Thijs van Leer is my all-time favorite.  Of course he's got all manner of classical training, but he's also an excellent jazz improvisationalist.

Elio D'anna-Osanna

Rainer Bodensohn-Brainstorm

I like Peter Gabriel's flute-playing a lot... it's very memorable.  Not that he's particularly very technically skilled at the instrument, but he does add a nice atmosphere.

Dellinger wrote: I like Thijs Van Leer pretty much. Focus was the first rock band (I didn't know about progressive then) which gave so much importance to the flute. Now, I don't really know so much about flute, is Ian Anderson really so very good? Or is he just in the most popular prog band fronted by a flute player? I mean, I really like his playing in Jethro Tull, but wouldn't know if what he's doing is really so amazing or just sounds cool.

     Ian Anderson blows most flute players away with his emotional playing.  His style, he created and it's been talked of in amazement by prog lovers since "Cross eyed Mary" etc. from "Aqualung.  He started the unigue style of playing so emotionally his breath in for more air to play sounds awesome and I've never heard the equal, as in purely emotional playing.  Ian with his band Jethro Tull also produced many folk inspired prog releases like two of my favorites, which include more traditional flute playing and he is still amazing.  Try the albums: Agualung, Song's From The Wood, and 'Heavy Horses."   Also, my favorite, "Thick As A Brick" if you like more straight progressive rock than folk inspired.  I have all of JT's releases except JTull.com.  I wouldn't go past "Songs From The Wood," as the quality of his music, or the style and times, made further releases very disappointing, exept for a few, like Stormwatch.  Still, I don't want to steer you wrong, so I'd get "Aqualung and Heavy Horses," to get the broadest overview of Tull's two major different styles, being straight hard progressive rock and progressive folk rock.  I won't even get into the first two releases, because they are much more blues based, and this was short lived.  Benefit, when Tull started changing to a heavy folk inspired prog band, is one of my fav's too, but I'd start with the 2 I mentioned, if you really want to hear an awesome flute player.