Originally posted by Depco:

Now I am having a problem with my PC client not being compatible with one or the other depending on if I have the mod installed or not. Is this where a Mod Manager would automatically select the correct mods for a specific server's mod list?

Not automatic by connection from the manager, but it's simple with r2mm on your client machine to just change the profile before launching the game and have it automatically change the mod files for it. In your case it would be even easier as it has "Launch Modded" and "Launch Vanilla" as independant controls, right next to each other on the same screen.