I recently got the Batman Arkham City GOTY for the 360. Here's what I found out with it:
- Standard version saves are recognized by the GOTY disc.
- GOTY version does not recognize DLC downloaded from the marketplace
- Standard version does not recognize DLC installed from the GOTY disc 2
Also, I picked up a copy of Portal 2 for the 360 that has a Platinum Hits sticker and a notice that it includes the Peer Review DLC. While this sounds as if it is included on the disc, it actually isn't, and there is an insert in the case directing you to download the DLC from the marketplace.
You also might want to add the Platinum Hits version of Left 4 Dead for the 360, which includes the Survival DLC (which was free), but none of the other, paid DLC. (Although, I just realized that Valve might've handled this like they did Portal 2, and not actually included it on the disc.)