I've only used the free version of Cyclemeter, which omits some features (auto-pause/resume). Good app for non-critical use, but, yeah, I've noticed some minor discrepancies. But the freebie Wahoo Fitness has the same quirks. It'll record slightly different distances for identical routes that I ride often.

I use them only for a rough gauge to my overall fitness, and to record rides I want to repeat -- or to remind me of routes to avoid!

I have no idea about elevation. I haven't figured out how to calculate grades. I just go by how it feels. There's only one hilly route near me and I can tell just from the gear I need and how much I'm huffing and puffing. Some days I can power up in a high gear, other days asthma slows me down and I granny-gear uphill.