I primarily use two mapping apps for field work related stuff on my iPhone and iPad, both of which are capable of doing what you want.
TopoMaps: $7.99
This app is awesome! You can download and store any USGS 7.5-minute quadrangle for the US or Canada (all maps are free, all you pay is the $8 for the app, which is incredible when you realize you might pay that much for a single paper map). You can see where you are on the map in real time, drop waypoints, import waypoint files from other devices, and export waypoint files from the app. Another nice feature is that if you are near the edge of a map the app will seamlessly join two or more maps together for viewing as one single map. If you use topo maps, this is the app to have.
GPS Kit (iPhone) and GPS Kit HD (iPad): $9.99 for iPhone, $14.99 for iPad
This is another great app and pretty powerful when it comes to creating waypoints and track files. It will let you cache maps from Google, Bing, and other sources for use when you don't have a network connection and it can import/export a variety of file formats. It has some other nice features like letting you store a photo of a location when you drop a waypoint.
I have both of these apps and use both of them regularly, they compliment one another nicely although either one will do what you are looking for. They both work great on the iPhone, but for anyone with an iPad they are truly amazing on there.