If you want to play literal retro games on PS3, there are a ton of compilations and otherwise straight ports. Too many to list here.
Here's my suggestions for a shortlist based on what you've said you're interested in
3d Dot Game Heroes
You already listed this, but yes - definitely get this
Costume Quest
A surprisingly decent halloween themed RPG; looks kinda childish but it's pretty fun
Digger HD
Remake of the PC game from the 80s, similar to Dig Dug
Braid
Puzzle Platformer with an interesting story/message to it
Little Big Planet 1 & 2
Both excellent games, highly recommend, especially if you can play w/ a friend/family locally
Catherine
Puzzle game with an interesting story and some really fun/challenging puzzle challenges post-game
Back to the Future, Sam & Max, Tales of Monkey Island
If you're into point and click I suggest all of these very highly
Any Telltale game series, Jurassic Park: The Survivors
If you're into point and click but don't like actually solving puzzles, these are far more story driven and very enjoyable
Mega Man 10
If you're into that sorta thing
Ico & Shadow of the Colossus
Both are available on PS3 and if you've not played them on PS2, these are straight ports with just a resolution bump, well worth playing
House of the Dead games
If you're into arcade light gun games HotD 3, 4, and Overkill are all enjoyable and available on PS3; they also support the Move controller if you pick one up, otherwise you can use a controller to move the reticle around the screen
Outland
Platformer with a polarize system similar to Ikaruga
Penny Arcade Adventures
If you're into the web comic, they made an RPG, and it's pretty good
Rayman Origins, Rayman Legends
Really great Rayman games
Ni No Kuni
RPG; I didn't like it but a lot of people love it, so you might
Dragon Fantasy
Series of RPGs, retro styled but with some modern accoutrements
Retro City Rampage
Parody of retro games and 80s/90s media, in the style of the original Grand Theft Auto (on PS1)
Double Dragon Neon
I'm not into beat em ups, but if you are you might enjoy it
Guacamelee
Metroidvania, but you're a Mexican wrestler
Trine
Action/platformer/puzzle game(s)
Pixeljunk series
Literally any of them, they made an array of games in different genres, all decent
South Park: The Stick of Truth
Pretty decent RPG that actually does kinda feel like you're IN an episode of SP
Rogue Legacy
Rogue-like platformer, really fun/addicting
Hotline Miami 1 & 2
Twin-stick shooters, but with an 80's vibe; VERY gory, and can be difficult at times. Shoutout to one of THE BEST soundtracks ever, across both games
Ultratron
It's what it sounds like - a modern Robotron
Lone Survivor
Pixel graphics horror game, actually really good
The Swindle
Really good platformer with some rogue-like elements
Thomas was alone
Platformer with a story about a... square.
Dragon's Crown
Beat-em-up with a cool graphics style
Spelunky
Rogue-like platformer
If there's a game in particular not listed here you'd like an opinion on feel free to hit me up. I've actually played a majority of the PS3 catalog.