Besides all mentioned above, you will probably want LARGE and reliable hard disks. RAID is also an option, especially for redundancy (RAID 1) because you will hold all of your music, all pictures and all video recordings on those disks and you won't be happy if you lose them. In case you are going for a RAID, look for motherboards that has integrated hardware RAID controllers. I'm however, using a different approach. I'm using two disks: one that is used for storing regularly accessed stuff (lots of read/write cycles that shortens disk's life) like root partition, swap file and TV cache and another, large disk for holding my HTPC data (videos, music, pictures, etc.). First one holds either stuff that I'm backing up on regularly basis (root partition with all programs and their configuration) or irrelevant data (TV cache) and if this disk dies, I can easily recover. Second disk is however too precious to be lost but also to large to be backed up. So, I've decided to store on it data that is accessed only occasionally to prolong it's life, I'm replacing it with new model every year of so and I'm praying for its life regularly to the Gods of Mechanics :). If you have space for third disk inside your case, you may choose to make one large RAID 1 mirror instead of only one disk that I'm using for this purpose.
Optical drives are also important decision, but in the end the choice is yours: plain old DVD, HD-DVD, Blu-ray... For this reason I've intentionally bought case that has space for two optical drives so my future upgrades can be smooth.
If you want to add videoconferencing, or even surveillance capabilities to your Home Theater PC (why not - that's why modular and expandable design is for, anyway), you'll probably want some kind of web cam. My advice is to choose one with integrated microphone, because it eliminates the need for yet another dongling piece of plastic in front of your TV. Depending on the place you want to mount it, choose one with proper mounting abilities.
RAM is not a critical factor if you plan to use your HTPC solely for watching TV/video/music in which case even 512 MB will be enough. But if you plan to add support for gaming on your box, then equip it with as much memory as you can afford - it does not generate any noise, as opposed to high-end graphic cards and processors that you'll also want for gaming. Whatever you choose, just don't forget to keep your HTPC quiet by all means. If you can't make it both quiet and capable for running games, make it just quiet and buy a console :)
Although it's not part of our setup, TV which will be used as display for our Home Theater PC should by all means have DVI-D connector on it (DVI-I is also OK) or HDMI. Notice that "D" suffix in digital that stands for "digital", because DVI standard supports both digital and analog signals. Classical VGA D-SUB analog connectors are still widely used in middle-range LCD TV sets, so be careful to choose TV with DVI-D support. Cables connecting DVI-D output on your graphic card with HDMI input on TV exists and are relatively cheap. Of course, if you already have a TV and don't want or don't have money to change it, classic VGA D-SUB connector with decent cable and graphic card will also do. S-video and composite connections should be avoided if possible, because they, in most cases, provide picture of lowest quality and require complicated setup in graphical drivers. On the other hand, tuner and all the other fancy TV stuff is not so important for our setup, because our HTPC will do all the hard work for providing the picture itself and TV will be used solely as displaying device.
