The file is in UNIX text format, newlines as \n (backslash n) instead of \r\n (backslash r backslash n) as in Windows based systems, which may cause that if you open the file, you wont see nicely formatted lines but a long text line with black boxes between things.

Variable items are separated by newlines.

Entities (henchmen, agents, EG etc) have their variables grouped together. The first thing in the group is always the EntityDescriptionID line, from which the entity can be identified. Relevant entity variables are grouped together with three lines on a line (---). The end of an entitys data group is marked with an empty line (just a newline)

EntityDescriptionID's from 500 to 510 seem to be the henchmen. 511 and 512 and possibly more after them don't seem to exist, so they are probably reserved for additional henchmen.

LayoutSkin

PlayerName

GeniusEntityID

Cash

EntityAvailable 

WatchedVideo

DifficultyLevel

AlertStatus

m_pendingHintVids

Desert or Jungle, probably the type of island

Default is Alex. This probably doesn't affect anything.

This is the Entity ID number of the Evil Genius.

The amount of cash the player has

What entities are in the game. ex. EntityAvailable=500 means Moko is in

Probably indicates what help videos you have watched

The difficultylevel, from 0 to 2

Alert level, 0 for green, 1 for yellow, 2 for red

How many help videos are waiting to be watched (Not sure)