If you have problems running ZDoom, then patching your IWAD may be one solution. Patching your IWAD modifies and/or adds resources to your IWAD that may not have been compatible with or may have caused unintended effects in ZDoom prior to the patching. Patches are available at http://www.doomworld.com/classicdoom/info/patches.php and should come with proper documentation on how to use them and on what IWAD version to patch to what version.
While it is not always necessary to patch your IWAD in order to play, it is a necessity for online play and will aid you in running other source ports as well. ZDoom will run pretty much any version of an IWAD provided it has the resources that ZDoom looks for in it -- meaning the resource only has to exist. It could be a graphic of purple floopy flowers, and ZDoom won't care, but you may have adverse effects if your maps differ and you're playing with somebody else. Spawning into walls is one...
The Doom Wiki has checksums of all of the official IWADs and checksums of different versions, so you are able to check which one you have exactly and if you are up-to-date.