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What is your favourite space quest game?

I prefer space quest 4 personally.
I prefer #1, #2, and #3. Hard to choose between them though.
Space quest 3 is a great game, too bad that nobody made any remake. It has a great story.
I've never played the remakes, I prefer the original graphics and (especially) the text parser. The fact that there is no text parser in #4 is one of the main reasons I rank it lower than the first three games.
If fan games count, I'd go with Incinerations. Otherwise, Space Quest 4.

Incinerations is an absolutely amazing game. Even better because it's free. To NOT think of it as being officially part of the series is depressing
Space Quest V may be the better balanced. Sq1 and SQ2 have their historical importance and they have a very nice pure space opera mood, but the puzzle design is totally unfair and the amount of deaths are a thing that thanks God has been vanished from adventure games as it added nothing at all. SQ3 is beautiful, SQ4 is all over the top, SQ6 is sadly flawed. And SQ1 remake is also nice, perfect as an introduction.
In order...

Space Quest III
Space Quest IV
Space Quest V
Space Quest II
Space Quest I
Space Quest VI

Ask GoG to include all the original files!