Here's my list. I haven't watched every series but I've seen a good portion of them:

Fantastic Four (1967-1970)

Every episode is a direct adaptation of an issue of the comic. They're pretty faithful and it has a great cast.

Spider-man (1967-1970)

This is my favorite Marvel series hands down. Again, it directly adapts actual issues but they take some hilarious liberties with the animation. Great cast and the perfect voice for Spider-man.

X-Men (1992-1997)

Iconic opening theme to a fun series. This show is what really launched the X-Men into the mind of popular culture.

Spider-man (1994-1998)

Fun series with another catchy intro. Again helped introduce a new generation to the iconic character.

Iron Man (1994-1996)

Avoid.

Spider-man Unlimited (1999-2001)

An interesting take on the character though due to low ratings never really got to anywhere.

X-Men: Evolution (2000-2003)

A fresh take on the characters that still has its fans to this day.

Ultimate Avengers, Ultimate Avengers 2 (2006)

Incredibly dull.

The Avengers: Earth's Mightiest Heroes (2010-2013)

Just plain awful opening theme but the show itself was fantastic. It's a crime that it was cut short. The show that replaced it was...

Avengers Assemble (2013- )

Awful, lifeless cartoon adaptation of the MCU. Earth's Mightiest Heroes was full of character and charm, whereas this was just...dull.

Ultimate Spider-man (2012- )

I'm currently going through this series on Netflix. It's a fun take on what introducing Spider-man to the MCU would be like since Marvel still had television rights to the character. Now that they actually have the film rights, I hope the new movies can live up to this show.

Marvel Disk Wars: The Avengers (2014- )

Bizarre concept for a series that basically turns the Avengers into Pokemon. I was able to watch the first episode and was surprised by the decent writing and depiction of the characters.