To use a less grim example, cooking. Certain combinations of foods will taste better together than they will individually (i.e., B+L+T). Likewise, certain combinations of otherwise delicious food may taste wretched together (use your imagination). In part, this is what makes cooking interesting, that you can't just roll up all the best ingredients into a ball of 'win' and marinade it in awesome sauce, but you have to be mindful of how each ingredient interacts with the others. This also makes cooking a decent meal more complicated than equipping your party in nearly all RPG's.
Consider Final Fantasy IX. The game features an interesting system of passive abilities. Each character in your party can learn dozens of passive abilities, and can have several of them be in effect simultaneously at any given time. With that many choices, there is a staggering number of different combinations of abilities for even one character. Unfortunately, none of the abilities interact with each other synergistically, so choosing a set of passive abilities is often pretty simple; you're free to just choose your best abilities without worrying about how they interact with each other.
To be fair, there is one notable exception to this. "Auto potion" allows a character to use a potion (or high potion) out of turn after each time they are damaged, but even high potions heal too little health by midway through the game for this ability to be worthwhile. "Chemist" doubles the efficacy of certain items used by a character, but it still doesn't make those items good enough to warrant spending a turn to use them. Individually, these abilities aren't the greatest, but they complement each other such that they're viable when used together.
A game that uses a similar system much more effectively is Paper Mario: The Thousand Year Door. The player can equip Mario with both combat techniques and passive abilities, though in Thousand Year Door this done by equipping badges because Nintendo refuses to just call things what they are. Rather, they would have you believe that Mario simply wears his boyscout sash everywhere so he can constantly rearrange dozens of badges without poking too many holes in his overalls.
But the point is, many of these badges interact with each other in exciting ways. Finding one new badge in that games doesn't necessarily just give you access to one more effect, but may give you access to multiple new strategies, depending on what other badges you can combine it with. Some sets of badges may significantly change Mario's combat role, completely changing the basic battle tactics the player uses, or sometimes a group of 2 or 3 badges can make a badge combo where they have a powerful effect together that is qualitatively different from what they would do alone. In some cases, badges have subtle anti-synergy. A badge that helps you dodge attacks doesn't really play well with one that increases your defense, since every attack you dodge was an attack where your defense wasn't relevant.
The most notable badge synergy in Thousand Year Door is the 'Danger Mario' build. The game has many 'danger' badges, which have powerful effects that only trigger when Mario is almost dead. Individually, these badges are trash, since being 'almost dead' rarely lasts very long, as you'll generally either heal yourself or just die within the next turn. However, if Mario has all of the 'danger' badges equipped at the same time, then once you become almost dead, you become nearly unstoppable. The most important of the danger badges is 'Power Rush,' which increases your attack power by 2 (which is a huge boost in this game) when you're almost dead. The unfortunate thing is that with a little patience, you can buy as many Power Rush badges as you want, turning Mario into the Glassiest Cannon that ever there was and making the rest of the game comically easy. Like, kill-the-final-boss-in-one-turn easy.
So maybe Thousand Year Door takes synergy a little too far. But still. Points for trying.