is it okay to upload screenshots from a game which has been modified ?

for example, if the game contains new graphics and such.

You mean a hacked game, for instance? If so, no, it isn't allowed.

If it's an official update, not released separately as a stand-alone game: yes. If it's fan made or modded: no.

Depends on whether it's an official modification or not.

what about taking screenshots with the source port ZDoom for the Doom games then ? the only thing that does is increasing the resolution.

It's not allowed. The game must be presented exactly "as is", with no modifications. Official patches are allowed, though.

This is my favourite modified game screenshot.

That's a demonstration of the game's built-in editor, so I think it counts.

Even though the source is available, are the WADs released for free yet?

I would like for us to be able to say "yes", with the caveat that non-out-of-the-box shots be clearly labeled as not representative of the published product. As it is I've sent in correction requests for shots of fanpatched games with English subtitles to be turfed in favor of the authentic (but unintelligible to most of us here) Japanese ones.