Can one avoid losing everything on a Galaxy Nexus when applying a new ROM (safely)? The makers of most ROMs suggest that you do a full device wipe when moving from one ROM to another. I have also found this is usually good practice, so data from the previous ROM does not affect the new one. On my EVO 4G, this was not a problem, since wipes did not affect the SD card. However, my new Galaxy Nexus (Sprint) has no SD card, and is managed all on internal memory. Every time I do a full wipe (in TWRP and Clockworkmod recoveries) they erase everything on my device, including my SD contents (photos, documents, the new ROM I'm trying to install, etc.). 

This is quite problematic and annoying, as it requires much more time to manually backup my backups before flashing anything. 

Has anyone found a way to avoid this? By that, I mean is there a way to keep portions of data (preferably the faux "SD" portions) between flashing new ROMs?
You can use adb backup command to back-up everything to your PC. Use this manual on XDA for correct parameters.