My all-time favourites in this category is Chris Mulder's series.
Love Beyond All Measure While Clark is away on vacation in Smallville, Lois investigates a securities fraud, which results in her being held hostage by the man responsible. He's armed with kryptonite and threatening to kill both Lois and Superman. If Superman can't save her, what will Clark be able to do? (Yes, it's Lois taken hostage, but Clark is too later)
and the sequel:
Dimensions of Loving In this sequel to the fanfic "Love Beyond All Measure," Lois and Clark's relationship moves forward, creating some surprising revelations for both of them. Also, while investigating the events that led up to Lois' being taken hostage, they must face an old foe who's armed with a new and deadlier form of kryptonite. - in which Clark gets kidnapped.
A couple of my own stories, in case you're interested:
Faux Pas Clark offers his new colleague Lois Lane a bed for the night after she's mugged. It was supposed to be all above board, but one thing leads to another.... What *will* she think of him in the morning? - during this story Clark is kidnapped.
An Ordinary Man When Lois and Superman are taken hostage by Nigel St. John and then left to die, they soon discover more about each other -- and themselves -- than they ever expected. And a story Tank and I co-authored:
Strange Visitor - the Evil Vignette (guess who's responsible for the evil part?):
In this rewrite of Trask's entrance in the episode "Strange Visitor," something very unexpected happens, and Clark is exposed to the greatest threat he's ever faced. A Tank and Wendy (sort of) Challenge Vignette. A multiauthored story by Wendy Richards and Tank Wilson. - and in this story too Clark is kidnapped.
Hope this helps!
Wendy