<p>I find the autoindent style of Notepad++ a little weird: when I am typing on an indented line, I <em>do</em> want it to indent the next line after I press Enter (this it does properly). However, when I am on an empty line (no indentation, no characters) and I press Enter, it indents the next line, using the same indentation as the last non-empty line. I find this extremely annoying; have you ever encountered this problem and do you know how to fix it?</p>
<p>(Note: I'm editing HTML/PHP files.)</p>

To be honest, this to me seems expected behaviour. Blank lines are used a lot by myself to break up the code to make it more readable, having the program make me have to tab out again would be VERY annoying.
I can understand this as a frustration with something like Python, but not with PHP... Though, before braces etc etc this might be annoying.
Try out
Komodo Edit
however, it's free, and I've found that it generally has been the best for auto-indenting for me. It seems to have learnt my coding style (or have the options in it for all coding styles and it picks up what you're using) and automatically indents everything correctly.
Edit: As you've noted in your reply, the issue is with "trailing whitespace" - I don't know Notepad++ too well, but most modern editors designed for coding have a "strip trailing whitespace on save" option (I know Komodo does!)