Just to reassure you, Apple doesn't use any proprietary formats. It uses AAC for music, which is the linear successor for MP3, allowing for bookmarking, multiple art, and arguably better quality at smaller sizes. Many other devices and programs use AAC as well (even Zune!). iTunes will also convert to MP3 for legacy apps/hardware if you need it to.
For video, Apple uses MP4 H.264, which is becoming increasingly common as it's used by Blu-Ray and other recent video players/systems.
iTunes DRM is proprietary to Apple videos (music is now DRM-free), but that's the fault of the myopic movie industry and Amazon, Netflix, etc. all suffer the same burden for their DRM.
You may be experiencing duplicates for a couple reasons:
1. You've dragged the same file into iTunes more than one time.
2. You've set in preferences for iTunes to copy music to its location, and then manage music.
The simplest way to avoid this is only add a song to iTunes once, and if you're copying it, delete the original copy from its location immediately thereafter.
Once you've already go duplicates, Jamesus advice above is the way to go.