The second screen of the menu Options\Preferences lets you set the colors for MesNews :

Zone Show information groups (in servers bar) :

Here you can set the colors for the groups in the menu's of the servers bar, according to the messages:

Info new messages (tree view) : when the group has other unread messages than the last synchronized, then the chosen color will be proposed. When you leave a group with unread messages this color will be used till the synchronization find new messages.
Synchro : direct answer to message : when the group has followed up messages (one of your messages or a conversation marked as follow up) and when there is a direct answer then the group will be shown in this color. This option is only valid for synchronized groups (at least subject-headers)
Synchro : answer in followed conversation : when an answer arrives in a group, followed up conversation, (or a conversation you replied to, of a conversation marked followed up) then the group will be shown in this color. This option is only valid for synchronized groups (at least subject-headers)
Synchro : other new messages : if a group finds by the sync new messages an if there are no followed up messages in this group this is the color that will be shown. In case the group is synchronized to only download the amount of messages this color will be shown also. (this sync does not allow the downloading of the body's of messages )

zone Infos new messages (treeview):

Here you can set the color of the groups in treeview, according to the messages in the tree. This setting gives the same information in the servers bar :

Info new messages (menu) : when the group has followed up messages (on of your replies to conversation or a message marked to be followed up) and there is a direct reply, it will be shown in this color. the option is only valid for synchronized groups (minimum subjects-headers)
Answer in followed conversation : when there is an answer on in a followed up conversation (a conversation you replied to, or a conversation that was marked to follow up) the group will be shown in this color. Option only available for synchronized groups (minimum subjects-headers)
Other new messages : If at sync of the group new messages are found, and these conversations are not followed up, the group will be shown in this color. In case of syn that only download the amount of messages available this color will be shown. (this sync does not allow the downloading of the body's of messages )

Zone Miscellaneous :

Central bar, when the group has new messages : the central bar of MesNews shows information about the chosen group. When a group is synchronized and new messages are available the bar will be shown in this color.
Group/server selected as per menu : choice of color that allows you to see quickly a selected group in the servers bar.