There are a few Neopets that can't be obtained through the "Create a Pet" option. They are either Restricted Neopets or Limited Edition Neopets. However all pets can be obtained through Transformation and Morphing potions and Magical Plushies..
Limited Edition: Most of these pets can be obtained through the "Create a Pet" option but only a restricted number is available to be created.
Restricted: These special Neopets will never be released through the "Create a Pet" option and must be obtained through a different method.

Name: Krawk
Type: Restricted
How to Get: You must first have a Krawk petpet and attach it to your Neopet. Then take it to the Fungus Cave and feed your petpet some fungus. This will then turn the Krawk petpet to a Krawk Neopet!

Name: Draik
Type: Restricted
How to Get: To get a Draik you must first have a "Draik Egg" in your iventory. Take the Draik Egg to the Draik Nest and it will give you the option to hatch it into a Draik Neopet.

Name: Cybunny
Type: Limited Edition
How to Get: Every year on Easter and Cybunny Day, a bunch full of Cybunny will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option!

Name: Tonu
Type: Limited Edition
How to Get: Every year on Tonu Day, a bunch full of Tonu will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option! However it has been noted that Tonu gets released randomly throughout the year.

Name: Poogle
Type: Limited Edition
How to Get: Every year on Poogle Day, a bunch full of Poogle will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option! However it has been noted that Tonu gets released randomly throughout the year.

Name: Jetsam
Type: Limited Edition
How to Get: Every year on Jetsam Day, a bunch full of Jetsam will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option! However it has been noted that Tonu gets released randomly throughout the year.

Name: Chomby
Type: Limited Edition
How to Get: Every year on Chomby Day, a bunch full of Chomby will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option! However it has been noted that Tonu gets released randomly throughout the year.

Name: Koi
Type: Limited Edition
How to Get: Every year on Koi Day, a bunch full of Koi will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option! However it has been noted that Tonu gets released randomly throughout the year.

Name: Kiko
Type: Limited Edition
How to Get: Every year on Kiko Day, a bunch full of Kiko will be released. If you are lucky enough, you will be able to get your own through the "Create a Pet" option! However it has been noted that Tonu gets released randomly throughout the year.

Name: Grundo
Type: Restricted
How to Get: The only way to create a Grundo is through Virtupets Space Station.