What is best

[Dek thorne]

I have some reclaimed hand hewn timbers and I am wondering what is the best way to go about squaring the ends.

[fishfighter]

You could level out a piece of plywood on top of the beam and past a circle saw for a cut and finish out with a hand saw.

[ChugiakTinkerer]

You would want to pick one face of the timber as your reference face and make the cut square to that.  Other faces may not be true for the entirety of the timber.

[loganworks2]

Google line rule timberframing. It will give you all the information you need. 

[timberwrestler]

What the last guy said.  If you want to be a lot more precise, then snap lines that are 90 degrees to each other down the length.  Then square off of those lines.