As we’ve witnessed the rise in price of the holy grail old back era cards, a lot of newer collectors (this guy) have been priced out of most of the rare/scarce old back trophy cards. Collectors will eventually have to adjust their holy grail cards to those at a more reasonable price point (relative to the 97-99 Pika, SSB, TMB). The attention will most likely shift towards some of the less scarce old back trophy cards and some of the super rare new back trophy cards. My question is, with all of the different trophies/prize cards in the new back era (eg Wonder Platinum, Master Key, Champions League, Pika Ring, Master Scroll, Players Club Espeon/Umbreon), what would you consider to be the Big 3 (Fantastic 4? Fab 5?) of the new back era trophy cards? Would the Neo Spring Battle Road numbered trainers be considered a new back era trophy even though a some of the copies were printed on e-reader/new back cards? Excited to hear everyone’s thoughts especially as a new collector looking to dive in head first to trophy cards!
Choose one of which you love the art and history 
Master’s Key - Master Scroll - Umbreon
IMO
There’s no doubt that Master’s Scroll is the most popular, and decently rare. But many of the others are rarer.
So it really comes down to what people will value over time, but I think art/demand is a safe bet
Spoiler alert: I’ve already chosen lol (see latest pickup below). I just wanted to get everyone’s thoughts here!
Popularity
Mew Victory Orb
Pikachu victory ring
Masters key
Rarity
Champions league - the versions with Pokemon inside though both are rare
Masters key
Wonder platinum
Others:
Umbreon
Espeon
Master scroll
@chok and @minorkey have a guide on all the trophy/prize cards. Looking at the New Back section, my personal favorites are:
- Master’s Key
- Victory Ring Pikachu
- Victory Orb Mew
@hyruleguardian 's thread on a Master List of the Rarest Pokemon Cards has a more comprehensive list to choose from if you expand your definition of “trophy” cards to cards which are rare (they’ve defined it as less than 1k estimated distributed copies). Out of the new back cards from this list, I personally like the Master’s Scroll.
Honorable mentions for me would be the Wonder Platinum, Miracle Diamond, and Mysterious Pearl trio, the Espeon and Umbreon Play promos, as well as the normal Victory Ring/Orb.
There are 10 high profile New Back Trophies. The Top 10.
- Victory Ring
- Victory Orb (154 copies)
- Pika Ring (163 copies)
- Mew Orb (163 copies)
- 05/06 Champions League (24 copies)
- 07 Champions League (scarcest) (24 copies)
- Mysterious Pearl (81 copies + many more from a separate event)
- Miracle Diamond (90 copies)
- Wonder Platinum (rarest) (20 copies)
- Master Key (most desirable) (36 copies)
Then there are the Top 4 current Modern New Back Trophies from 2011.
- BW Victory Cup (40 copies for 1st/2nd and 80 copies 3rd place)
- XY Victory Ring (56 copies for 1st/2nd and 112 copies 3rd place)
- SM Victory Decoration (39 copies for 1st/2nd and 78 copies 3rd place)
- SS Victory Proof/Crown (still being awarded but so far 4 copies for 1st/2nd and 8 copies 3rd place)
The Master Scroll is more popular than the key. 
Umbreon in 10 would be the most valuable though yeah?
Super rare, you say?
If you want to throw jumbo cards into the mix, each of the 13 magazines which hosted the 2009 Design Contest awarded one copy of a jumbo card to each of the 5 runner-up entrants featuring their design. In total this means that there are 30 unique (1 of 1) jumbo Pichu cards and 35 unique jumbo Arceus cards distributed.
All of the cards mentioned in the thread so far typically have a copy appearing for sale every year, however as far as I’m aware none of the jumbo cards from the 2009 Design Contest have surfaced so far - and I can only imagine most very likely never will.
Not so much of a big 3, this is my candidate for a jumbo 65. 
Very true, but its ok for everyone to be wrong 
Mysterious Pearl, Mysterious Pearl, Mysterious Pearl
I once allowed myself to think that Master’s Scroll is overhyped because it doesn’t have a Pokemon on the card, big names & efour discord shilled it forever & it subjectively isn’t on the same level as the key, Miracle Diamond, Wonder Platinum or even some of the modern Pika trophies like Decoration & Proof, but then I woke up with a severed Ponita plush-head in my bed & saw @thundermoo and @winters pacing outside my house, so I came here to tell you that indeed, the Master’s Scroll is the best trophy card out there. It is really sparkly.
3rd place victory cups have the same copies as the 1st and 2nd place (no card awarded to 4th place winner). They started doing that with thr victory rings onwards
Big 3 new back definitely: 2007 Champion‘s league, wonder platinum and Master‘s key… at least for me…
The 2007 champions league is the hardest trophy card to find, period. Even harder to find than the old back ones…
Personally, I’d agree with the others that listed these:
Mew Victory Orb
Pikachu victory ring
Masters key
I think I’d put Key first, Pika second, and Mew third.
It’s weird to me to see the Scroll listed with the others because I don’t really think of it like that. Sort of just an expensive/popular promo. But having handled like, literally dozens (lol), it is a weird one to include. I think of it more similarly to the Mysterious Pearl.
As much as I love the miracle diamond, wonder platinum, and Champion’s league, they’ve always taken a backseat in popularity and I feel like they don’t wow as much. Not featuring Pokemon that are broadly loved makes them an easy lower rank for me.
But really, everything is second to the Key if we’re being honest.
Championship Arena – All aboard the hype train! lol
In all seriousness…
Master’s Key
World Championship Full Art Pikachus
and
Wonder Platinum
I think these three are going to be the toughest to obtain.
Personally…
Master’s Key
Victory Orb Mew (Because I nerd heavy on Mew like most)
Master’s Scroll