Using wrong character set

I might not be able to fully solve your problem, but I can explain some of what's going on. The shell is behaving correctly; TextWrangler is not coping correctly with a slightly advanced requirement.

In test.txt, you have an a (garden-variety lowercase letter A) followed by a combining tilde (Unicode character U+0303). Combining characters generalize characters with accents. For all intents and purposes, ã (U+0061 LATIN SMALL LETTER A followed by U+0303 COMBINING TILDE) should be equivalent to ã (U+00E3 LATIN SMALL LETTER A WITH TILDE).

Quite possibly, if Unicode was invented now, only combining characters would exist, and we'd always use a; but Unicode also has many characters for compatibility with earlier existing encodings. Because these are the characters almost everybody uses, many programs do not support combining characters so well, if at all. In particular, it looks like TextWrangler does not support them at all and shows a “I don't know what this is” mark instead.

Generally speaking, OSX prefers decomposed characters (i.e. letter + combining accent). In particular, as far as I know, all file names are normalized to this form. Normalizing file names (i.e. making sure that if there are several possible forms of a file name, then a specific one will always be used) is very useful, because it avoids being unable to find leão.png when you're looking for leão.png. (You don't see a difference between the two? Good, your browser handles combining characters correctly.)

The ideal solution would be for you to use an editor that handles combining characters correctly. If you want to stick with TextWrangler, make sure you have the latest version, and if you do, contact the authors for support. With TextEdit, jEdit or AlphaX, there's hope yet: they're showing the file as Mac Roman instead of UTF-8; try to switch them to UTF-8.

The "~" key is located between the "left shift" and "Z" keys on the international english keyboard.

Many users are used to have this key under the escape key (the US layout), and they (including me) use the KeyRemap4MacBook software to swap those keys.

Edit: KeyRemap4MacBook is now called Karabiner. Here is a screenshot of the configuration I'm using to remap Section to Backquote key.

Edit: Karabiner does not work on macOS Sierra, however a new project is in development: Karabiner Elements. As of now, it can do the replacement in question: