With x264, instead of specifying bitrate you can specify the CRF (Constant RateFactor) which will automatically adjust the bitrate to maintain the same visual quality throughout. I really recommend it because it means that, for example, if you have two scenes that are the same duration but one has much more motion than the other, the bitrates will be adjusted accordingly, whereas if you set a bitrate yourself artifacts may appear in scenes with faster-than-average motion.
A CRF between 19-21 is usually used by online TV/movie release groups.
I've found CRF 12 to be visually lossless for 480p content, and CRF 16 for 720p+ content.
This would allow you to easily set up 4 different profiles, like:
480p HQ: CRF 19
480p UHQ: CRF 12
720p+ HQ: CRF 20
720p+ UHQ: CRF 16
x264 is also higher quality than VC-1 at the same bitrate, due to cool compression techniques like
CABAC.
As for container formats, MP4 and MKV are both great for x264 streams. MP4 has the advantage of being more widely supported on renderers like TVs, BD players, etc. while MKV has less overhead in terms of both filesize and load time, which can make a significant difference with CPU usage on HD files. I would probably go with MP4 by default because of compatibility but offer a MKV option if you can be bothered, for people who will play the video on their computer.
My 2c
