Rachni in Mass Effect 3

It actually seems saving the Queen in ME1 and then again in 3, will be more beneficial to Shepard.

If Shepard did not spare the Rachni queen on Noveria, the Reapers will artificially construct a Queen thrall in order to control a rachni army. Shepard can choose to spare this artificial queen even if the Commander killed the real queen. This queen will eventually betray Shepard, taking the Rachni Workers War Assets away and decreasing the numerical values of some Alliance fleet War Assets.

As with all "plot" characters that die, they do get some form of replacement, it just so happens her replacement is much more sinister.

source

Personally, I saved the Queen, which, losing the Krogans sucked ('cept for Grunt's general awesomeness), provided a ton of War Assets added to the cause.