There's the "War Trash" quest series, which reminds me a lot of a Jack Bauer-esque storyline. You go undercover and work with the NCR to infiltrate a terrorist group. It's a whole lot of fun and if you're going to do an agent playthrough that's friendly to the NCR this would fit like a glove.
Bond is always sneaking around, so I'd also add the 'STUN' mod. It allows you to subdue, and tie up your enemies using rope, handcuffs, or duct tape. I'd highly recommend it, as it added a whole new stealth component for me.
I'd also add the CAM mod, which allows you to make things like poison, and tranquilizers. You can then either sneak up on the enemy and inject them with the chem, or shoot them with a dart filled with it. I think it's a useful mod and since weaponized chems seem to be a recurring theme in spy stories, you might want to use it on your playthrough.
DISCLAIMER: These two, I haven't tested - so download at your own risk!
There's also the "Agents Arsenal," which gives you a non-voiced James Bond follower among other things. You can see a full comprehensive list of what it adds on the site. There's another weapon mod called the camera gun, which is a silenced .22 disguised as a camera. Very bond-esque, if you ask me.