It appears as if we can't show/hide items based upon the amount entered in a user defined price. For example it would be nice to show the credit card fields if the user defined price is > 0.
Also I have a similar issue with confirmation emails where I would like to be able to show certain messages based upon the amount given from a user defined price.
That is correct. You can't use the user-defined amount in conditional logic. How about if you added a checkbox for the user defined amount to say "Other amount?" and when checked, you reveal the credit card fields?
You should be able to use a conditional shortcode in the notification. See this documentation: http://www.gravityhelp.com/documentation/page/Shortcodes
You could do something like this:
[php]
[gravityforms action="conditional" merge_tag="{Donation:7}" condition="greater_than" value="1000"]
Thank you for your donation of over $1000.
[/gravityforms]