There are many of Jesse's games that I have not been able to identify. Those with access to a 4K version of Breaking Bad and greater familiarity with NTSC/U Xbox 360 packaging may be able to help.

ATTACK POINTS-
Multiple Xbox 360 games appear out of focus on Jesse's shelves in S4E8.
A stack of Xbox 360 games is shown as Jesse is playing Sonic 06 with Brock in S4E11, Crawl Space, though they are obscured by Jesse's collection of empty DVD cases.
Many Xbox 360 games are strewn on Jesse's table during Jesse, Walt and Mike's meeting in S5E1 (most visible when Jesse suggests magnets).
There is also an unknown Xbox 360 game beneath a stack of boxes and the rear of a PS3 game partially shown beneath Jesse's DVD of Open Season 2 during the ricin cigarette search in S5E2.

Working on this at the moment - first find is that he appears to incongruously have Rainbow Six Mission Pack: Eagle Watch for PC amongst what I'm assuming is a stack of music CDs, unless that one to the right is a game I'm not recognizing rather than an album.

@DJSCheddar Excellent, thank you

I don't know how sure you want to be on these but I'm fairly convinced that in this (rotated) picture, 3rd from the bottom is FEAR and 6th from the bottom is Viva Pinata: Party Animals

Gears of War under the mystery one on top here

Herculean effort. Thank you.

This one under Open Season appears to be Infamous 2

Spectacular, thank you

I have a friend who religiously watches that Sonic 06 scene over and over again. It's his favorite thing in the world. That's the most I know about Breaking Bad outside of playing Breaking Bad 64 with a Guitar Hero controller (it's surprisingly playable(

Btw, if you wanted to include more comprehensive comments for my additions that are more in line with your own:
- Rainbow Six was in a stack of other jewel cases on top of Jesse's sound system when he and Walt meet in S4E8. FEAR and Viva Pinata are in a stack on his shelf in the same scene.
- Infamous is on his coffee table during the cigarette search in S5E2 and Gears is on his TV stand up in his bedroom in the same scene

Also, Star Wars: The Clone Wars for original Xbox visible on Jesse's shelf as Walt searches it in S5E02, as well as a sadly unidentifiable game in a generic GameStop case.

The following also appear to be on Jesse's shelves during the cigarette search:
- Brink (top of horizontal stack)
- NBA 2K10 (4th down)
- GTA3 for original Xbox (5th down)
- Tao Feng (6th down)
- Ghostbusters: The Video Game for Xbox 360 (farthest left on vertical stack)
- Unreal Championship for original Xbox (with a sticker cutting off the end of "Championship", 4th or 5th from the right in the vertical stack
- to the right of that, a Sega Sports game for original Xbox, almost certainly NBA 2K3 or NHL 2K3, but those games' spines are so similar it's impossible to tell with this quality of image

@DJSCheddar Incredible contributions, as always.
I'm fairly confident that the third game from the top in that shot is Virtua Tennis 3. Looked up a few more that I thought were possible, but I just don't know the US spines well enough to recognise many myself.

this is one of backloggd's crowning achievements

Incredible work