Analyze my game with ....

what software?

I used to use my notebook and board, but now I imagine there is some software that can hold my repertoire along with possible combination/traps etc. Everything I've looked at lacks this feature. 

A free Graphical User Interface (GUI) for chess is Arena. See: www.playwitharena.com

I used winboard for years and know my way around the old versions better than arena but there are a number of GUI's out there. Then you can install differant chess engines and the top chess engine these days is stockfish, that happens to be free and open source. See: https://stockfishchess.org

.pgn is a file standard for chess games that can include notes and sub variations. I use Fritz for a GUI with Stockfish loaded as the main engine. Chessbase is great for keeping your games orginized and preparing for certain players you have in your database. Chessbase lite is a free download.

If you are in Brookings tomorrow I can show you everything on my laptop.

http://www.sdchess.org/flyers/2015/2015-Jackrabbit-Open.pdf

Grab a USCF membership at uschess.org to save time registering in the morning at the tournament. Hope to see you there!

ChessBase and Chess Assistant are good options. I have used ChessBase but not Chess Assistant yet and I have heard good things about Chess Assistant.

Use Brain 1.0 and silicon only for blundercheck afterwards.

I've used most the options given, especially ChessBase. These are well and good for deep analysis, but for recording games they are clunky and awkward. I write software and know how I want my GUI to look. I just haven't found it yet amongst chess software. Guess I have to write my own. 

...no chess software until you reach 2000 OTB.