This feature was added to mIRC as a UI option without a command to compliment it.

Originally Posted By: versions.txt
20/10/2012 - mIRC v7.27

Changes:
1.Added "Mark As Read" menu item to treebar, switchbar, toolbar and MDI popup menus to clear all flashing/highlighted window icons.

However, it's very easy to script yourself. You use the command /window -g0 on a target window to change the switch/treebar color to black. Use it in a loop to apply this to all windows, or windows of a specific type.

Here is an example alias for marking all windows of every type across all server connections, as read. If you need it adjusted to only affect specific window types, let me know.

ALIAS MarkAsRead { var %i = 1 | WHILE ($scon(%i)) { scon %i | var %j = 1 | WHILE ($window(*,%j).wid) { window -g0 @ $+ $v1 | inc %j } | inc %i } } ; by Raccoon

Well. At least I won lunch.
Good philosophy, see good in bad, I like!