Ninja Baseball Bat Man - Arcade - Irem: I discovered this one recently, as it wasn't in any arcade I ever entered during my younger years. I must say that Ninja Baseball Bat Man is the most ridiculous thing I ever played and it is still all kinds of fun.
Knights of the Round - Arcade/SNES - Capcom: Capcom had a way with this genre in the early 90s, and Knights of the Round was one of their high water marks. Everything about this one screamed quality, and it never got old.
Target Renegade - NES - Taito: The direct sequel to the game that spawned Double Dragon, River City Ransom, and and other classic games, Target Renegade is everything you should want in a Beat Em Up. It's tough, fun, and last just long enough for you to feel good about popping it into your NES.
Final Fight(series) - Arcade/SNES/Sega CD/NES/Saturn/PS2 - Capcom: The game that started life as Street Fighter '89 had enough legs to stand on it's own. Final Fight gave birth to a big chunk of the cast of the Street Fighter Alpha series, an excellent 8 Bit retelling of the original game in Mighty Final Fight, and sadly spawned two minor turds in Final Fight Revenge and Final Fight Streetwise. All in all, the Final Fight franchise is the stuff gaming dreams are made of.
Streets of Rage(series) - Genesis/Mega Drive - Sega: Sega was at one point known for bring their cutting edge arcade titles home, but this series was rooted in the rise of Sega's 16 Bit consoles, the Genesis and it's European/Asian counterpart, the Mega Drive. The series was known for it's crisp gameplay and thumping soundtrack. The high water mark for the series had to be second game, which was so widely praised that it shipped with the system for a while. Fans have been clamoring for a new game in the series for a while, so maybe Sega can partner with Platinum games and deliver.
TMNT: Turtles In Time - Arcade/SNES - Konami: The first arcade game featuring the Ninja Turtles was good, but Turtles in Time may possibly be the measuring stick by which all Beat Em Ups are compared. Everything about Turtles In Time was magic attached to a controller, and not even that horrible remake from Ubisoft could change that fact.
Battletoads(series) - Same As Double Dragon - Tradewest: The original game in the series is in all honesty one level (Turbo Tunnel) away from being quite honestly the best game in the genre, period. The only reason the game hasn't seen a sequel is that bloggers keep complaining about the difficulty so much that Rare(who developed the original game) thinks it would be a disaster to put it out. I honestly don't blame them either. Gamers are crybabies now.
Guardian Heroes - Sega Saturn/XBLA/Game Boy Advance - Treasure: For a developer like Treasure, a lot of your catalog can be considered high water marks in a genre, but Guardian Heroes was a GENRE DEFINING release at a time when good Beat Em Ups were becoming hard to find. Guardian Legends not only featured great gameplay, but also inserted branching paths, multiple endings and a karma meter for high replayability.
Castle Crashers - XBLA/PSN - The Behemoth: Part Gauntlet, part Crime Fighters, and part Alien Hominid is the best way I can describe Castle Crashers. It may have been the first thing that really made me want to pay money for Xbox Live. It's that great.
Metamorphic Force - Arcade - Konami: The best Konami Beat Em Up not attached to a license, and there are little gnomes in it like the ones in the Golden Axe series that can be beaten up for powerups.
Golden Axe(series) -Pretty Much Everywhere - Sega: Before Sega Developed the Streets of Rage games, their big entry into the Beat Em Up category was a homage to the days of swords and sorcery called Golden Axe. Sega's ubiquitous barbarian tale has spawned several sequels, including a Master system RPG, a Saturn fighting game, and a horrid 3D action game on the PS3 and Xbox 360.
River City Ransom - NES - Technos Japan: A Beat Em Up with RPG elements? Those two things shouldn't mesh well, but in River City Ransom they did in masterful fashion. It still holds up as one of the best games on the NES and one of the best games in the genre, period.
I didn't mention a few games in the list (The Simpsons, The Punisher, X-Men) Mainly because those are always mentioned. I love those, but I wanted to mention lesser known games like Ninja Baseball Bat Man and Target Renegade because they deserve it, and let's be honest, it's my list, so I can name what I want. These were a few of my favorites of the Beat Em Up genre, but if you want to add to the conversation, feel free to do so.