For the spy, he should have an air-pistol that can hold eight rounds in one magazine but has to be cocked after each shot, thus having an even slower fire rate than the sniper's rifle. The rounds don't do any damage, but they can make the target dizzy and hallucinate, taking away much of the player's control over his/her character's movement and the use of his weapons. Also the targeted player won't be able to see his/her surroundings and where he/she is going due to the effects of the rounds, thus buying the spy enough time to dispatch his opponent and/or get away from the situation.
Another weapon the spy should have is a ballistic knife, which is a knife that can fire off its blade. It won't do as much damage as the butterfly knife (also known as the balisong), but it can do ranged damage and can be used while cloaked. However, the blade cannot be retrieved when it hits its target, and the spy has to go to a resupply-cabinet to get another one (he can get it back if he misses). Also, the blade has limited range, and its trajectory is parabolic, like that of the syringes from the medic's syringe gun.
For the engineer, he should be able to build a heavy machine-gun nest that other players of other classes can use. However, it can only be built on certain locations (for example, the bunkers at 2Fort), and they can be used by opponents as well.