G, C, or something else?
High D ! 
I think, nevertheless C
Eb
second that. Maybe Bb as well, a Boehm Alto flute is to a Bb flute what a normal Boehm is to a D.
Thirded.
Eb - for the following reasons :
a - great for solo playing,
b - you occasionally come across sessions where the pitch is a semi-tone sharp,
c - many commercial flute recordings are made using Eb-pitched instruments,
d - if you want to play along with Highland pipes, or learn tunes from their recordings.
Most popular: Eb, definitely.
But like many people in the beginning of 19th century, my own favorite would be F & Bb. (Remember AndrewK’s F Rudall… Wow!)
Eb, and, like Henke said, Bb is becoming somewhat popular (on recordings, at least). Henke, not sure what you mean with the Boehm analogy…Boehm alto flutes are pitched in G, and a regular Boehm flute is still basically built around a D major scale…in the key of D, the only fingering difference between a Boehm flute and a simple system flute is the F#, and that’s simply due to the Boehm flute’s key mechanism (the F# being in the acoustically proper place and therefore being unreachable by the fingers–thus the need for intervening keywork).
Is that G as a bell note with a four-key foot (equivalent of a long B foot on the normal Boehm)? If not, and if you are right. I was wrong. I tought the lowest note on a short foot Boehm alto flute was Ab, adding one more key, long foot, would give G, and the highest note on the body, excluding the foot keys would be Bb. Don’t know where I got this from, and it might be wrong, but I was just pretty certain of it, until you commented on it.
Anyway, talking about simple system, Bb is becoming very popular. Many of the finer players record Bb recordings, mainly for the low key, haunting voice. Lot’s of slower stuff on Bb.
I love Bb Flutes and Fifes are always in Bb so that is in a way a popular key.
Henke, a long foot on an alto flute would add a low F#. But if an alto flute is considered to be in G, the same logic would say the regular flute is in C (not D, as I said above).
why?
I’ll toss in my views here. Eb gives a flute which is much more responsive, and makes crisper ornamentations. The pitch difference is not very big to the ear, so an Eb still has most of them sound characteristics of a D flute, but easier playing with more responce.