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Here's a selection of fanfictions that have stuck to my mind. Like all recommendations, this is all very subjective. Our tastes may differ widely. For example, I'm not a Sam/Jack shipper or of the Romance genre in general, so don't expect to find many of those in this list. Slash, on the other hand... These are external links, unless otherwise specified.

Accidentally on Purpose, by PZawadzki
Just because I'm not a Sam/Jack shipper at all, doesn't mean that I won't enjoy a well-written one. This one is from Jack's POV. It's funny and sarcastic like only Jack can be.

Ciphers, by Destina
A story on language, and how it can hurt Daniel. The plot is just beautiful. Destina's prose is enthralling. It's Jack/Daniel (pre)-slash, though this story is an excellent read even if you're not into slash.

Fine, by Sylvia
A tag to "Evolution". Hurt/Comfort. Quoting Sylvia: "Dang it, I wanted some comfort with my hurt. Since the Stargate writers didn't deem fit to write it." More show than tell, which is why I like it.

First Contact, Last Encounter, by JB
My nails will never recover from this story. This tag to "The First Ones" is, in my opinion, more stressful than the episode itself.

Grounded, by Kormantic
Jack/Daniel slash. A bit desperate, and very hot without being porn. My favourite passage is quoted below (highlight it if you want to read it now, otherwise head straight to the fanfic).
>>Jack curled his fingers around Daniel's forearm and squeezed. Daniel's eyes went from blurred and lost to narrow and intense fast enough to make Jack's mouth go dry.<<

Two Sides of the Coin, by Dith
Jack/Daniel slash. A potentially squicky fic that toys with non-con, but I liked it. The settings are excellent, as are the original characters, although Jack is off by moments, in my opinion. It's dark, violent, and erotic.
My reactions just after reading it (LiveJournal) >>