My runtime environment is always *nix, so for me, perl's default "chomp" behavior is to remove just a final "\n". When I'm writing a script that might need to handle text files from both *nix (LF) and ms-windows (CRLF), I use the following instead of chomp:

s/[\r\n]+$//
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Because I use macosx a lot, I also sometimes see text files that use just CR instead of LF. Then there are cases where a file isn't consistent in terms of its CR vs. LF vs. CRLF behavior, or where a file wasn't originally text data, but has been mishandled (corrupted by a "unix-to-dos" text-mode conversion as if it were text). It can get pretty maddening, so I wrote a script just to report diagnostics, and posted it here in a SoPW thread several years ago: Re: How to determine type of line endings in a text file from within a script

It boils down to the problem of getting to know the data you're dealing with, and taking appropriate steps to give it the treatment it needs.