• @newlinks is not cleared between documents.
• Any data HTML::LinkExtor accumulates is not cleared between documents.
• @links is ever growing.

Unrelated problems:

• Using foreach to loop over an ever-growing array is not recommended. ("If any part of LIST is an array, foreach will get very confused if you add or remove elements within the loop body.") Use a while loop instead.
• When using $p->parse, you need to end with $p->eof.
• The "skipping" check should be done on absolute uris.
• @visited should be a hash to avoid the "skipping" loop.
• /$domain/ is not a safe method to accomplish the desired option.
• URI should be used instead of URI::URL.
• $newlink should be declared where it's used.

Update: Added the foreach problem.
Update: Added the $p->eof problem.

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