The Ruling Skill Challenges articles in Dungeon could use some of your thoughts! They've been very good, with ideas how to change up the bonuses provided by Secondary Skill rolls, but your idea of carrying the bonus outside of the Skill Challenge and into other areas (such as combat) are great, too.
Just as a list that I've gathered, here's some ideas on how to do more than just "add a bonus" (this list includes possible penalties, too):
- secondary skill successes grant bonus to primary skill checks (+2 to +4)
- cancel out 1 failure in the skill challenge
- reroll any one skill check (potentially, you could add to this "take the better/worse roll")
- grant an automatic success at any point in the skill challenge (important to note "at any point" because that's better than just "on the next skill challenge roll")
- receive an automatic failure
- penalty on next check, -2 to -4
- success allows a totally new event to happen, allowing a new skill to become primary, which if in turn is a success, circumvents some other part of the Skill Challenge
- drop or decrease the DC of one of the primary skills by one level (hard -> moderate -> easy)
- force a reroll, take the current roll
- apply a very specific bonus to a certain circumstance (+2 on Diplomacy against a dwarf)
- failures cumulatively increase the tension of the situation (i.e., every 2 failures raises the alert status of the town watch by one; each raise of the alert status provides penalties to skills such as Stealth or Bluff, because the watch is more active)
- failure triggers a random encounter, which might have special constraints due to the skill challenge (time-limit, force the players to flee, patrols are increased in the area, etc.)