Can you please be a bit more specific, commanderted?
First, are you referring to the general black-blue Apogee boxes used for a certain time to ship mail orders?
Because this are the only official ones I can think of in terms of boxed releases.
All other boxes are local variants of different publishers.
Second, which boxed copies including which games (important) selling for which prices have you seen lately?
For some $20 is already insane for an old game while others say $200 for a rare game (box) is ok.
And e.g. a mail order of Wolf3D in the generic Apogee box is of higher value as Blake Stone, … .
But to add a short answer already:
Apogee games are awesome and boxed copies of it are even more awesome