What is the best way or most used way to do anamorphic encoding?
Crop and then set 4/3 or 16/9 in mkvmerge?
Or is there a certain way to do this with x264's --sar?
There really isn't a quick and easy way to answer this, aside from posting a link without any explanation, as demonstrated above.
If you're encoding only for software playback (in mplayer/MPC/VLC/etc), either method will work, and you don't really need to worry about it (provided you give the correct SAR/DAR numbers of course).
But if you want this to work on hardware devices/players, you'll first have to know how they handle the video. Some
make it really difficult for you to tweak how video display ends up, and in general
not all hardware will do this the same way. Truly MKV-compliant players should pull the DAR info from the
mkv container (as set by mkvmerge), while most other players will pull the SAR/PAR from the
video stream (as set via x264 --sar). Setting AR in the video stream will probably work better on hardware players in general, although in my experience encoding to mkv directly from x264 seems to set both.
Also, I sometimes see that Blu-Ray encodes are sometimes not 1920x1080/1440x1080/1280x720/960x720. Is this because when you crop that you leave the resolution as is and do not mess with the aspect ratio?
Yes. If you do not crop to scale, you will not end up with the same aspect ratio. For example, if you take off 10 pixels vertically and 10 pixels horizontally from a 16:9 video, the resulting video will not be 16:9. You'll have to recalculate the DAR in such cases.