This question or answers to it will likely contain spoilers.
In the series so far there have been a lot of allies who may have been killed. In general, it is usually better to help your allies to live and meet whatever criteria are required to ensure you have as many allies as possible.
As I started my game I wondered: Are there any reasons to prefer specific characters dead? I mean the first thought that comes to mind is someone gets possessed by a reaper later and makes a boss fight ridiculously hard, or someone turns on you for some other reason. In addition to allies, are there any NPCs who your actions may have saved in previous games, that might have been better off dead?
Best Answer
There is a very specific benefit for killing off Wrex in the first game:
It is described in this answer.
Another very minor point:
You have to kill off Morinth (if she counts as a party member) if you want Samara to be in ME3, as Morinth does not show up in ME3 at all.