[SEO - linking to empty sites]

Punishment sounds not logical because it are external factors. SEO is search engine optimization with no content this will be hard you might only be able to rank on the domain name. But if you want to know for sure just test it 

[wordpress comment pagination with foreach loop]

I had this bookmarked from sometime ago it might help you.

 

http://www.catswhocode.com/blog/how-to-integrate-a-pagination-in-your-wordpress-theme

[the "upgrade your browser" campaign]

This is Avant browser. The font looks a lot cleaner and readable than on Firefox. The CSS doesn't work.

 

On Chrome it almost hurts my eyes

[Newbie with a gifted code...]

Could be part of anyway this is certainly some kind of config of something there is no output generated for the client.

[Toy Museum Update - 3 Designs Opinion]

#3 the others are to dark, I would only change the menu a bit so it is a bit more clear.

[CMS recommendations]

One that is simple and quick to use is Wordpress. I wouldn't recommend Joomla, for the more bigger/complex sites I would recommend Drupal. Offers much more options and is better on areas as SEO and security.

[FTP Programs]

FilleZilla, it's opensource and easy to use

[First Ever Website]

For a starters site it isn't bad how ever I have some criticism or how ever you wanna call it:

 

# The homepage should consist more text.

# On HD resolution you got a very wide website menu on the left content at the right.

# I noticed some 404 errors, this should never happen on a live site.

# Personally I wouldn't add the "best viewed in FF.." in the main menu.

# You don't use any headings tags like h1 and h2.

# Title tag is stuffed with to much text.

 

About the design, I like basic designs so for me it is okay how ever try to align everything on the right position.