How to analyse Games

I very much agree with bb_gum. Stay away from engine analysis, which in my experience is typically awful, other than for finding tactical wins 3-5 moves deep.

The methods I've always used in conjunction for analysis: (1) Look at the book moves, understand why the book moves are "best", see where the game deviated from book, and look for refutations, either immediate or deferred. (2) Do tree analysis, which is obvious. Find the part of the game where you were clearly losing, and/or weren't doing very well, and backtrack to see where you went wrong, since if you had played perfect moves, you would be doing fine throughout. (3) Do logical analysis, in the style of Silman's books, which is to say: just think through the position, especially its imbalances. For example, if your opponent has a doubled pawn, figure out which piece would be best to attack it, then how to get that piece down to its attacking square/line. Or if your opponent lost a tempo, figure out which book move you would normally play, and why, to optimize your attacking chances. Or if your opponent has the bishop pair that is becoming powerful, figure out where to place your knight or remaining bishop to trade off one of his bishops. The list of things to check is very long.