1. read them in
2. find all the words (as determined by /\b\w+\b/ ... there are other ways)
3. print out of all the unique words and how often they appeared
4. print out how many words there were total

Right? Ok ... I come in at 81 characters. 78 for the code and 3 for the switches.

#!perl -nl
END{print"$_ ($w{$_})"for sort keys%w;print"\n$t"}s/\b(\w+)\b/$w{$1}++
+;$t++/eg
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It's basically a rewrite of your code, with a few enhancements.

73 (70 + 3 for the switches). The \b's are pretty much unnecessary and using $& means you don't need parens.

#!/usr/bin/perl -nl
END{print map("$_ ($w{$_})\n",sort keys%w),$t}s/\w+/$w{$&}++;$t++/eg;
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Sh?aving seven strokes:

#!/usr/bin/perl -lp
++$t,++$w{$_}for/\w+/g}for(map("$_ ($w{$_})",sort keys%w),$t){
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One might wonder why you're using s/// to replace something with itself rather than just using nested while loops and a m// instead.

while( <> ) { while( /\b(\w+)\b/g ) { $w{$1}++; $t++; } }
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Update: Duh, you're going for obfuscated not efficiency. Never mind me.

It's also golfier ... try golfing my reply down without using s///eg ...

Being right, does not endow the right to be rude; politeness costs nothing.
Being unknowing, is not the same as being stupid.
Expressing a contrary opinion, whether to the individual or the group, is more often a sign of deeper thought than of cantankerous belligerence.
Do not mistake your goals as the only goals; your opinion as the only opinion; your confidence as correctness. Saying you know better is not the same as explaining you know better.

Looks like you checking for the frequency of words in a file. In that case, the 2 \b in your regex aren't really necessary.

s/(\w+)/$w{$1}++;$t++;$1;/eg while (<>);
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Just throwing this one out there for fun and to show a different approach:

#!/usr/bin/perl -nla
INIT{undef$/};$w{$_}++for@F;print"$_ ($w{$_})"for keys%w;print"".@F
# 345678 1 2345678 2 2345678 3 2345678 4 2345678 5 2345678 6 234567
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67 + 4 = 71 strokes

#!/usr/bin/perl -0nla $w{$_}++for@F;print"$_ ($w{$_}) "for keys%w;print~~@F small correction :)

#!/usr/bin/perl -0na
$w{$_}++for@F;print"$_ ($w{$_})
"for keys%w;print~~@F

there is literal \n at the end of second line