As far as Protagonist monsters I much preferred Elemental Heroes as they offered the most variety by being based on a group of monsters as opposed to a single one.

As far as I know stardust dragon was the first of them I saw growing up to the franchise itself

ha ha le gay Kuriboh & al his frenz O nd Watapon (Nd time wizrad, red eyes, celtic guardian, gamma the magnet warrior)

Shapesnatch

Mokey Mokey

Don't forget Firewall dragon, but well my favorite would be dark rebilion, clear wing, and cyber monsters.

I assumed this was like a poll-type thing with a few options. As for favorites in general. Ojama Green. Just.... Ojama Green

Time Wizrad is the fave

Blue-Eyes White Dragon. Not only is it hyped up to be an ultra powerful card (and it was strong, although soon outclassed by other things), but it was also owned by THE Seto Kaiba. Plus, that 3000 atk is nothing to sneeze at, so you always expect a clever trick to get around him. It's also got some neat support such as Maiden with Eyes of Blue.

My personnal favorites were Black Skull Dragon in DM and Flame Wingman in GX. I also liked Junk Warrior, Gagaga Kaiser and Enlightment Paladin. Vrains' Code Talkers are also pretty cool.