Here's a few suggestions and bugs I've noticed. You may be aware of most of these already.

Markdown in guides.

Only display "Tools Guides Saves Splits Modifications ROMHacks" if there's actually content there. Make a seperate submission page where you can submit these kind of things if it's hidden?

individual_levels page doesn't show the other co-op player, as seen here: http://www.speedrun.com/lcgol/individual_levels . Sometimes there's a random comma. Also players without a website account aren't displayed on that page.

The 'Tools' page should allow you to link an external url instead of uploading a file.

The 'Splits' page needs mime types set for .lss files. If user uploads one right now and downloads, they get plain text.