In the Lost in Space intro why was Dr. Smith actor listed as a special guest star?

At the point where Jonathan Harris joined the show, everyone else had already signed contracts that said where their names would be put on the billing, so he unfortunately would have to be last. As consolation, he negotiated to be listed as a "Special Guest Star" because it was "ridiculous", according to what he said at New Jersey's Chiller Theatre Expo in 2001:

I called a friend of mine who was head of casting at NBC and I asked, "Have you ever given billing, in all of the series that you've done, to somebody for whom it will say, every week, Special Guest Star Jonathan Harris?" He said, "Don't be silly! I wouldn't give billing like that! That's ridiculous billing! It doesn't exist!" And at that time, it did not exist. I said, "THANK YOU! That's all I need to know!"

I called Allen and said, "I solved your billing problem." "Eh? What?," said Mr. Charm. I said, "I will accept last position: Special Guest Star Jonathan Harris." Well, the next 20 minutes you would not have believed! "YOU GODDAMN ACTORS YOU CAN'T ACT ANYWAY! NONE OF YOU ARE WORTH A NICKEL AND I'VE GOTTA PAY ALL YOU BASTARDS!!!" And on and on. [Laughter.] I didn't open my mouth! I just sat there and listened. "YOU CAN'T ACT ANY OF YOU. YOU'RE THE WORST OF ALL, YOU CAN'T ACT AT ALL!!!" On and on. I took a deep breath and said, "OK!" and hung up. Amazing! That was the first time that kind of outvie billing occurred. Now, of course, billing is total madness: "With the Special Appearance of ... With the Appearance of ... With a Cameo Appearance of ... " I started that whole crap!
_{Never fear, Smith is here!}

Jonathan Harris did not join the cast of Lost in Space until after the show was already in production, not being in the pilot. At this point the billing had already been finalized, so through contract negotiations, he was able to be billed as a 'Special Guest Star' for every episode. According to him, starting the entire "Guest Star" billing in television period.

As from the Interview Transcribed here.

I called Allen and said, "I solved your billing problem."

"Eh? What?," said Mr. Charm.

I said, "I will accept last position: Special Guest Star Jonathan Harris."

Or if you care to listen, from the horses mouth. Here is a direct mp3.

Smith wasn't in the show as originally conceived (or in the original un-aired pilot). When the show did go to air with a re-worked pilot (in which he sabotages the ship), it was originally thought that his character would be a short-term villian (per this article on Wikipedia), accounting for his "special guest star" billing. Due to his popularity and flamboyance, he was kept on and the billing continued as it was.