Here's my top 10:

10. Super Paper Mario

9. Super Mario Bros.

8. Paper Mario

7. Super Mario 64

6. New Super Mario Bros. Wii

5. Paper Mario: The Thousand Year Door

4. Super Mario World

3. Super Mario Galaxy

2. Super Mario Sunshine

1. Super Mario Bros. 3

I can never seem to give a short responce with these kinds of things so my apologies ahead of time if I rant a little.

 

There are a few top contenders, but in the end I have to go with Bowser. He was originally simply the "boss character" but has evolved greatly as a character. He can be a genuine threat (Mario Galaxy) but then prove to be the series best source of comedy (the RPGs).  He's obsessed with world domination, but is still a caring father. His never-ending quest to defeat Mario has grown into something of his way to prove his worth to himself and the universe. Nintendo plays on his role as antagonist in such subtle but effective ways. It's easy to just say "Bowser's the bad guy again" but Nintendo has found away to turn what would otherwise be a cliche into character development, it's just a shame more people don't see the complexity that Bowser has become.

 

 The close runners-up for me are Mario himself (because he's Mario), Luigi (for similar reasons to Bowser, but to a lesser extent), Wario (he makes me laugh), Rosalina (a tragic Mario character? Cool), Geno (he's like Gandalf and Buzz Lightyear in one) and Fawful (because he's the mustard of your doom).

 

I guess I also could have listed DK, Yoshi, Peach and Kamek, but then I'm not really narrowing it am I? Ooh, but I should give Diddy Kong a mention if he counts, because DKC2 is one of my favorite games, and also, duh, monkey with a boom box! 

SloganYams

Your paragraph about Bowser explains why I like him so much. :D