The first fics that came to mind were two by one of my favorite authors, Shayne Terry. Actually,
Fugue is about Clark with amnesia; it's the sequel,
Fugue 2: Fusion that has the reference to The Annihilator. Shayne actually manages to work in a lot of other stuff as well, including alt-Clark finding his alt-Lois, what would have happened if Sam Lane continued to work on cyborgs, and the evil NIA agent Trevanian. Don't miss it. It's better in the nfic version found on Annesplace.net.
Otherwise, I couldn't recall any fanfics off the top of my head related to this episode, so I went to the Archive Database.
Pamela Mariano wrote a very short vignette - an alternate ending to the episode in
The Biggest Surprise of All . Jana Lippe wrote *two* alternate ending fics,
Alone At Last and
Really Alone At Last .
Stacey Wong found her inner muse and told the episode in verse, in
The AKA Superman Poem .
The only other episode-related fanfic listed in the Database is a good one by the gifted Alicia U. In her
AKA Clark Kent she tells us something about being married to Superman - he's always running off. Not just to save people (OK) but for charity events and appearances (not OK when you're Lois Lane and you're desperate for a little nookie.) Again, this is a fic best appreciated in its nfic incarnation, found on Annesplace.net.
