It is perhaps easier to describe "unclean" code. For example:

• Code with lots of code smells (see also wikipedia Code_smell)
• Lots of magic numbers
• A 5000-line main program
• A sub that reads and writes global variables
• A sub that does not have a single purpose; for example, instead of a sin function and a tan function, someone defines a sin_and_tan function
• Some of a sub's parameters are not used
• A sub that is 1000 lines long, aka "Big-Arsed Function"
• Duplicated code
• Code with gaping security holes
• Code that leaks resources
• Code that is not thread-safe or signal-safe

Conversely, some clean Perl code attributes are:

• strict-safe
• warnings-safe
• taint-safe
• Good variable naming
• Minimize variable scope
• Prefer lexicals to globals
• Good commenting
• Consistent indentation and visually pleasing layout
• Easy to understand
• Simple, Clear, General
• Easy to use module interfaces
• Comprehensive test suite

Finally, TheDamian's new book Perl Best Practices provides much sound advice on writing clean Perl code.

Update: See also Is it correct? by GrandFather:

• Does it work correctly?
• Do you understand it?
• Would anyone else understand it?
• Will you understand it in a month's time?
• Does it strike a good balance between terseness and verbosity?
• Could you make changes to it without it being likely to break in unforeseen ways?
• Is it fast enough?

Update: See also: On Coding Standards and Code Reviews and Re: I need perl coding standards (Coding Standards References)