I have a Tivo S3 and 2 cable cards. Integration is perfect. The S3 only supports Single Channel CCs, so I need 2. The Tivo HD supports multi-channel CCs, so you only need one.
The big worry now is SDV. There's some sort of a USB dongle planned to allow the Tivo S3 and Tivo HD to do the 2-way communication needed to get an SDV channel, but it isn't ready yet.
TW has started implementing SDV. You could lose the ability to tune into SDV channels if your cable system implements SDV and you have a tivo hd or s3 with cable cards. (same with any cable-card enabled device).
I think SDV stands for Switched Digital Video. It basically allows the cable company to put less-used channels on on-demand SDV frequencies, so they can multiplex more channels using the same bandwidth. When your box or cable card tunes to an SDV channel, it has to request that channel from your local distribution node, which allocates bandwidth for it and presumably tells the box or cc what frequency the channel is on.
The dongle is supposedly in the pipeline, but nobody knows exactly when it will be available.
Oceanic TW has already implemented it on Oahu and the Big Island, but not yet on Maui. My fellow OTW tivo hd/s3 owners on Oahu and the Big Island have lost several HD channels until they can get the dongle. Broadcast HD, HBO and SHO are non-SDV. Everything else HD moved to SDV, including HD Theater, Nat. Geo, ESPN and ESPN2, TBS, HDNET and HDNET movies, etc). Some of the channels like TBS, ESPN*, Nat Geo, etc have normal digital variants that are still available, but some of the others are hd-only channels. OTW won't even sell you the HD package that includes only the SDV HD channels if your only outlet is via cable card right now.
-David