Mysqld.exe memory usage
Please note that your server seems to have recovered from a crash, according to the init log. Something strange may have happened there related to your problems (a crash, a non-clean stop, a memory leak, etc.)

There are several reasons why MySQL 5.6 may be consuming a lot of memory (specially compared to 5.5). 

You have a 128Mb buffer pool (default), that may consume around 150 MB of memory having into account the extra buffers. Aside from other global buffers, you have to add the per-connection memory. You have a huge join_buffer_size on your configuration (128M), but it is commented. Make sure that it is not set to that value by executing:

SHOW GLOBAL VARIABLES like 'join_buffer_size';


Anything bigger that 4MB is normally not recommended.

The first one I would check, however, -which several people have reported memory problems with- is the performance_schema, a new feature that has been enabled by default in 5.6. You can check its memory consumption by doing:

SHOW ENGINE PERFORMANCE_SCHEMA STATUS;


For more information, we would need the runtime statistics of the server, namely:

SHOW ENGINE INNODB STATUS;
SHOW PROCESSLIST;
SHOW GLOBAL STATUS;




Edit to your edit

Do not set the Buffer Pool to 4 MB! That is a global value, and the most important cache buffer if you are using InnoDB.  That is too little even for an embedded system. The 4Mb was just for the join_buffer_size. If you don't know what to put there, and as you seem to be aiming for low memory usage, set it to something around the 50-80% of the total memory you aim to consume.

Your performance_schema consumption is certainly worrying. Set performance_schema = off on your configuration and restart MySQL Server.

Regarding per-connection-memory: simply you must know that there are some variables that reserve memory per action or per session. join_buffer_size, sort_buffer_size, etc. are session variables; innodb_buffer_pool_size is global to the server and is only reserved once. If you are using a single connection to the server, you may not have to worry too much. But please share the complete output of the previous commands, and your hardware specs/memory usage aims.