Bust-a-Move 3000

Super Puzzle Bobble gameplay is essentially the same as the rest of the series. It bestows some audiovisual improvements, adds and removes gameplay elements, adds a new art style, and adds a new character roster. It has single player, training, computer competition, and two player competition modes. New to this game are large-sized bubbles and a two player cooperation mode, in which players work together to solve a stage.

The GameCube All-Stars version has a four player option and a Space Invaders-style mode called "Shoot Bubble".

The PlayStation 2 and Game Boy Advance versions received "generally favorable reviews", while Bust-A-Move 3000 received "mixed" reviews, according to the review aggregation website Metacritic. In Japan, Famitsu gave it a score of 28 out of 40 for the PS2 version, 24 out of 40 for the Game Boy Advance version, and 26 out of 40 for the All-Stars edition.

Ryan Davis of GameSpot said the PS2 version has the best graphics and sound of the series to date, "with extraordinarily sharp 2D graphics and a healthy amount of visual splendor", but that its gameplay represents an "incredibly stripped-down" disappointment to the series which "brings virtually nothing new to the franchise" and is missing a lot of features from the previous year's Bust-a-Move 4. As for BAM3000, there was nothing new and the analog controls were awkward, but the multiple gameplay modes kept players happy. Geraint Evans of NGC Magazine regarded the game as worth owning, but only on one console. Tom Russo of NextGen found the Japanese PS2 import a bit disappointing and no different from the original game.