Egocentrism inclines me to think that apps were written for me. Reason leads me to believe they were not.
Apps can gain access to all sorts of information inaccessible to the browser.
Most common reoccurring problem I find is that all links off-site, are displayed in a webframe. Which doesn't give me access to the normal things that Safari does - I can't email the page, add it to my reading list, or bookmark it, so inevitably I always open it in safari. I'd've rather stayed there in the first place...
But this is not the only sin, just the one that leaps to mind.