The Marrying Man (aka Too Hot Too Handle) (1991) and The Getaway (1994)
The venomous post-marriage discourse between Alec Baldwin and Kim Basinger has rendered their onscreen collaborations morbid affairs indeed. Their first film together is a justly forgotten comedy, but their second cinematic pairing is an underrated crime thriller directed by Kiwi filmmaker Roger Donaldson (The World's Fastest Indian, No Way Out).
A remake of the 1972 film starring Steve McQueen and Ali Macgraw (overshadowed in its own time by an affair between the leads), The Getaway one of the few gritty 90s crime thrillers to live up to the gauntlet Tarantino threw down with Reservoir Dogs. Worth seeing for the french fries scene alone.
Eyes Wide Shut (1999)
Director Stanley Kubrick said ahead of time that his plan with Eyes Wide Shut was to cast a real-life Hollywood couple as the film's married lead characters, then cause them to split up. Mission accomplished, Stanley! I would argue that this underrated film isn't overshadowed by the subsequent divorce of its lead actors, and is maybe even enhanced by it. It remains the defining aspect of the project for most people, however.
Proof of Life (2000)
Like The Getaway, this is a decent genre film that didn't deserve to be overshadowed by the short-lived tabloid-friendly affair between it's lead actors, Russell Crowe and Meg Ryan, who play characters who also sort of have an affair. The kidnapping thriller has some great stuff in it, and is worth a watch, but good luck thinking about anything but Crowe and Ryan kissing behind the bike sheds.
Gigli (2003)
We can't blame Gigli's awfulness entirely on the assiduously documented relationship between leads Ben Affleck and Jennifer Lopez, but the pairing certainly played a role. Their second collaboration, Kevin Smith's Jersey Girl (2004), is also a perfectly terrible film in its own right.