There are quite a few major organizations in the Mass Effect universe, many of which the player either works for or goes up against in combat as they progress through the series. Some of these groups are notably more evil than others - Cerberus, for example, is a major antagonistic force in Mass Effect 1 and is arguably one of the largest threats to the galaxy in Mass Effect 3.
The Mass Effect trilogy features an in-game codex that players can look through for context on various species, locations and corporations introduced throughout the series. One section of the codex is dedicated to organizations, and there players can find a general overview of the companies they're associating with - or, in some cases, fighting against. Some organizations, such as the ExoGeni Corporation in Mass Effect 1, play a minor role in the series, while others return consistently across all three games.
Players should also consider talking to each of their crewmates in order to hear varying opinions on some of the organizations introduced within the series. Miranda and Jack, for example, have vastly different views when it comes to Cerberus. These opinions also have a tendency to change as the trilogy progresses. Garrus starts out as rebellious in ME1, and as a result he's initially firmly disillusioned with C-Sec. His interactions with Shepard across the Mass Effect series can change this viewpoint if players make certain choices. Objectively, though, certain organizations are undeniably morally questionable at best.
Evil Mass Effect Organization: Eclipse
A mercenary corporation introduced in Mass Effect 2, Eclipse is featured in various missions across Omega and Illium throughout the course of the game. Although the group largely focuses on smuggling, Shepard discovers in ME2 that each new Eclipse recruit has to commit a murder in order to join up with the organization. Players will have to deal with the Eclipse in both Garrus and Samara's recruitment missions, as well as during Thane's loyalty mission in Mass Effect 2.
Evil Mass Effect Organization: Blue Suns
Although players will encounter multiple mercenary groups across the Mass Effect trilogy, the Blue Suns are arguably the most prominently featured. Multiple recruitment assignments in Mass Effect 2 involve Shepard facing off against the organization, as do several of the crew's loyalty missions across the game. Zaeed Massani, one of the DLC companions included in Mass Effect Legendary Edition, is one of the initial founders of the group - and his ruthless efficiency and disregard for civilian casualties arguably embodies the company perfectly.
Evil Mass Effect Organization: Blood Pack
While the Eclipse and Blue Suns favor at least some form of discretion and stealth, the Blood Pack mercenaries instead prefer simple tactics more along the lines of beating their enemies into submission. The mercenary group mainly consists of Krogan officers and Vorcha cannon fodder in ME2, and their gang war with the Blue Suns is featured in several quests across Omega in Mass Effect 2. The group is banned from Citadel Space, so Shepard can primarily only encounter the professionally violent organization on planets like Tuchanka.
Evil Mass Effect Organization: Cerberus
First introduced as a terrorist group in Mass Effect 1, Cerberus is the primary organization featured in Mass Effect 2 and one of the major antagonists of Mass Effect 3. A pro-human and objectively anti-alien syndicate, Cerberus operates off the grid under the leadership of the Illusive Man. Cerberus is responsible for assassinations, experiments on both human and alien subjects, and - in Mass Effect 3 - sabotaging Shepard's attempts to destroy the Reapers. Although players are temporarily allied with them throughout Mass Effect 2, they progressively become more and more antagonistic throughout the course of the Mass Effect series.