I posted this on the old board in the middle of a thread, but I can see a few people are confused about which ponies belong in which wave and what number we're up to so I though I'd post again. I hope this makes sense and is useful. 

The single brushables are shipped in boxes of 12 assorted ponies (including duplicates and repeats) from Hasbro to the toy retailers, and each different box of 12 represent a wave.

Below are the waves so far, the brand new ponies each time are in purple.

Wave 1
2x Applejack
2x Fluttershy
2x Pinkie Pie
2x Rainbow Dash
2x Rarity
2x Twilight Sparkle

Wave 2
2x Cheerliee
2x Lily Blossom
2x Applejack
2x Pinkie Pie
2x Rarity
2x Twilight Sparkle

Wave 3
2x Blossomforth
2x Cupcake (US)/Sugarcup (Euro)
2x Dewdrop Dazzle
2x Lulu Luck
2x Fluttershy
1x Pinkie Pie
1x Twilight Sparkle

Wave 4
2x Feathermay
1x Flitterheart
1x Honeybuzz
1x Plumsweet
2x Snowcatcher
2x Twinkleshine
1x Applejack
1x Rarity
1x Rainbow Dash

Wave 5 - Travelling ponies (with luggage)
2x Applejack
2x Fluttershy
2x Pinkie Pie
2x Rainbow Dash
2x Rarity
2x Twilight Sparkle

Wave 6 - Travelling ponies (with luggage)
?x Cherry Pie
?x Diamond Rose
?x Applejack
?x Pinkie Pie
?x Rainbow Dash
?x Twilight Sparkle

? almost certainly meaning 2 of each but I haven't seen anything to confirm that yet.

There seem to be some oddities, like with the inclusion (or not) of the promotional DVDs or the removal of fringes, but I haven't seen anything yet to suggest that the single ponies are being sold in differently configured assortments than those detailed above. But I happily alter the list if someone has more information.

It seems that Hasbro are keen to make sure that the Mane Six stay pretty easy to get hold of, but the new pony distribution does seem oddly haphazard to me!