There are many ways to format URLs in Markdown. Parentheses work better with some methods than others.
1. Bare - http://example.com/test(1).html
2. Bare, encoded - http://example.com/test%281%29.html
3. Delimited - <http://example.com/test(1).html>
4. Hyperlink - with <a href="http://example.com/test(1).html">parens</a>
5. Markdown Link #1 - with [parens][1]
6. Markdown Link #1 - with [parens at end][2]
7. Markdown Link #2 - with [parens](http://example.com/test(1).html)
8. Markdown Link #2 - with [parens at end](http://example.com/test(1))
- Bare - http://example.com/test(1).html
- Bare, encoded - http://example.com/test%281%29.html
- Delimited - http://example.com/test(1).html
- Hyperlink - with parens
- Markdown Link #1 - with parens
- Markdown Link #1 - with parens at end
- Markdown Link #2 - with parens
- Markdown Link #2 - with parens at end
Note also that parenthetical sections in MSDN links are optional, so:
http://msdn.microsoft.com/en-us/library/5471dc8s\(VS.80\).aspx
could be linked to, instead, as:
http://msdn.microsoft.com/en-us/library/5471dc8s.aspx
See also The Problem With URLs for Jeff Atwood's blog post about coming up with a solution for Stack Overflow.
Other issues with URLs
Sometimes URLs can fail to link correctly because they contain disallowed characters. In these cases encode the characters using the % notation. Previously characters such as () [] ' and * were not allowed but the server-side Markdown renderer has been modified to accept them now. Currently the only (known) characters that aren't accepted are ones with accents, graves, diaeresis, etc. For example: é or ö, although if it's a Wikipedia link you can just use the unadorned character. (A suggestion to have these characters supported has been made on UserVoice.)