Yep it's the raw folder format that you get when ripping without Cobra enabled. It was the first way we had to play games. It's been outdated as it isn't as easy to use as Cobra ISO files. I can't think of one instance where JB folders are better then ISO.
JB folders are better in these scenarios:
1- If you need to rip the files to reduce the size of the game... After do it, you can convert the ripped game to ISO.
2- When you keep the DLC and update patches of the game in PS3_EXTRA. You need to unpack the ISO if want to add more content.
3- If you want to play these games in non-Cobra CFW (and without Mamba)
4- JB folders are better for game modding
5- For games like SingStar that use content from other discs.
For any other case, ISOs are better

- NTFS support
- Better net_host support
- Better compatibility
- Faster file access
- Easier to check game integrity (e.g. MD5)
- Support large files (>4GB) on FAT32
As the title suggests, what are the difference of these two? Because I've been seeing games that have PSN version and non PSN version.
PSN version are signed as npdrm with klicense (free or non-free).
Retail version (non-PSN) are games ripped from BD disc and the files do no use a npdrm klicense. So the executable files (EBOOT, SELF, SPRX) can be decrypted without a rap/rif.
PSN version use *.edats, retail use *.sdat to pack some data.
PSN version come in PKG files and are always installed on internal HDD. Using external gameDATA tool it's possible to install them on USB FAT32, if the game don't have large files (>4GB). Some games have hardcoded the path /dev_hdd0 in the EBOOT, SPRX or SELF files.
Retail version come in DISC format. However the update patches are in npDRM format with free license. The DLC are also npDRM and can be free or paid (require a rif/rap).
The demos are npDRM free. The C00 are full games PSN format that are activated by an .edat license (Rebug and PS3HEN can bypass it). The paid content (PSN) require a rif/rap.
For some games, the EBOOT and some other files of the PSN version and retail version (generally the EBOOT of the update patch) are interchangeable. This is the principle used by the CFW2OFW tools.