Once upon a time, a company named Atari had a video game console named the Atari 2600. Perhaps you've heard of it. Unfortunately, Atari's hubris and a flood of incredibly mediocre games (including ET and the infamous Atari 2600 version of Pac-Man) had killed the video game industry dead by 1984. This story is told elsewhere, but the fiery death of Atari had consequences.
One of consequences was Nintendo's caution with the NES, especially in the US. Among Nintendo's many draconian protective measures was a hard cap on the number of games a company could produce each year; Nintendo figured that if companies could only make five games a year, they'd have to be good. (This didn't always happen, but that's neither here nor there.)
Thing is, five games isn't a lot, for prolific developers and publishers, like Konami. Several successful publishers, including Konami and Acclaim, were straining under this limit, and petitioned Nintendo to allow them an exception. Nintendo did, by allowing those companies to publish additional games through semi-autonomous subsidiaries. Acclaim used a toy company they had purchased a couple years before (LJN), and, in 1987, Konami founded Ultra Software Corporation (a.k.a. Ultra Games) as a go-between to get around the limit.
The Ultra logo is familiar to many NES owners from the time. It's simply "ULTRA" in bold white sans serif captials, with a series of thin red horizontal lines superimposed. "Games" in small grey capitals is below "ULTRA", aligned to the right.
Ultra would publish the NES Metal Gear, the various Teenage Mutant Ninja Turles games pre-SNES, a couple games developed by none other than Sid Meier, and several Star Trek games. Additionally, Ultra published the DOS ports of the NES games released under the Ultra label, and several Game Boy games related to the Ultra NES games.
Despite being essentially a cheat around Nintendo's rules, Ultra did develop a game in-house. When Konami decided not to release Hideo Kojima's sequel to Metal Gear, Metal Gear 2: Solid Snake, on the NES, Konami of America chose to have the localization team at Ultra develop an original Metal Gear game. The result, Metal Gear 2: Snake's Revenge was a bomb, critically, commerically, and quality...um...-ally. The developers couldn't capture the balance between action and stealth, and gamers noticed.
By 1992, Konami was developing exclusively for the SNES and Nintendo's strict publishing rules had since been relaxed, so the farce was unnecessary. Ultra folded in 1992, and the remaining staff was absorbed into Konami of America.
The Ultra games, in alphabetical order...
This list may be missing some NES and Game Boy titles, and is definitely missing some DOS ports. /msg me with any missing games.
Sources: Mobygames and lots of public knowledge.