To be clear here, you only want stories with humans vs. aliens, and you want it to be war, not just “sapients versus fierce but unintelligent animals”, right?
Another good (well, mixed-bag) setting to check out is The Fleet, a shared-universe anthology in several volumes written by a variety of different authors. Multi-author anthologies like this are also good for figuring out which authors you like, so you can seek out more by them.
Oh, and not to neglect the classics: Make sure to check out Enemy Mine (the novella, not the movie). Humans aren’t exactly the supreme butt-kickers of the Universe, but we’re dishing out about as good as we’re getting. The story is really more about the peace than about the war, though.
Babylon 5 had this as a recurring theme. The humans were one of the more powerful spacefaring races (they are the 4th or 5th strongest, depending on how you decide to balance them against the Narn Regime). The humans (or factions of them) end up in wars involving far more powerful enemies. When all else fails, the humans are described as being remarkably tenacious fighters (at least a few EarthForce ships are shown meeting their ends in flames, ramming enemy ships to take them down with them) and not above using germ warfare, nukes, and assorted booby traps to defeat or destroy their enemies.
Well, it’s actually a web original (though not a fanfic), but Stuart Slade’s The Salvation War fits pretty well.
Basically, in early 2008, Yahweh himself sends a message to the people of Earth, saying that he’s finally forsaken humanity, and allowing Satan to send his armies to claim the planet, it’s people, and their souls for himself.
The collective response from the survivors (a number of the more devout monotheists obediently killed themselves, went catatonic, or simply lost the will to live and spontaneously died), is basically “screw the both of you, and the horses you rode in on.”
“Let me tell you something about Hew-mons, nephew. They’re a wonderful, friendly people – as long as their bellies are full and their holosuites are working. But take away their creature comforts… deprive them of food, sleep, sonic showers… put their lives in jeopardy over an extended period of time… and those same friendly, intelligent, wonderful people will become as nasty and violent as the most bloodthirsty Klingon. You don’t believe me? Look at those faces, look at their eyes…”
Quark, “The Siege of AR-558”, Star Trek: Deep Space Nine.
Quark had a lot of great insights on the humans on DS9.
Quark: I think I figured out why humans don’t like Ferengi …
Benjamin Sisko: Not now, Quark.
Quark: The way I see it, humans used to be a lot like Ferengi: greedy, acquisitive, interested only in profit. We’re a constant reminder of a part of your past you’d like to forget.
Benjamin Sisko: Quark, we don’t have time for this.
Quark: You’re overlooking something. Humans used to be a lot worse than Ferengi: slavery, concentration camps, interstellar war. We have nothing in our past that approaches that kind of barbarism. You see? We’re nothing like you… we’re better.
A non-OP thanks for everyone’s suggestions here. I’ve started reading a few - Brin’s Uplift, Drake’s Ranks of Bronze, and Zahn’s Pawn’s Gambit and they’re uniformly excellent so far. There’s nothing like some human patriotism (is there a word for this?) SF to counteract my innate misanthropy