My all-time favorite iPhone app is RadarScope. It's an elegant little app that parses the raw NEXRAD weather radar data feed and renders it -- faster and more efficient than downloading the already-rendered radar images from the National Weather Service or wherever.
It also uses Location Services to track current position and can automatically choose the nearest weather radar. I'm doing a long trip next May and plan to mount my iPhone on the handlebar with RadarScope running so I can keep an eye on weather that's in my path. In the past I've just kept the phone in my pocket and checked RadarScope when taking a break, sometimes adjusting my route or schedule according to what the radar is showing. But on a long trip it would be nice to have more immediate access to this information.
To keep service records on my bikes and car, I use Road Trip.
Campwhere is a great app for finding a campground -- it's got virtually all public campgrounds, from national parks down to city campgrounds.
GreatestRoad is a nice little app for collecting excellent stretches of road.
I'm still looking for an ideal GPS app. I want one with quality offline maps, but the few existing apps that include maps are very automotive-focused. The TomTom app, for example, does not allow route planning with more than a single viapoint.