my @variables = $_ =~ m/<\?--(\S+?)-->/g;
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One really minor nitpick: $_ is the topicalizer and as such it is implicit in many operations, wich makes for terse syntax. So one either wants a fully qualified variable name like $line and thus

my @variables = $line =~ /<\?--(\S+?)-->/g;
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or

my @variables = /<\?--(\S+?)-->/g;
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  for my $variable ( @variables ){
    # replace the tag with the value of the variable
    # if there is one.
    s/<\?--$variable-->/$$variable/g if $$variable;
  }
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One major nitpick: I would've ++'ed your node for mentioning another WTDI, complete of interesting considerations, but I --'ed it since you're unnecessarily using symrefs whereas we warn newbies all the time about the risk of doing so. It just amounts to using the symbol table as a generic hash, which is a good reason to use a specific one instead, e.g. %value. Failing to do so you should be prepared to cope with some corner cases: what if he as a <?--0--> or <?--$--> tag? Well, unprobable enough, granted, but even without that putting all values together in a separate structure is saner. The OP is clearly a newbie, so he may read your example as advocating symrefs and take them as a programming habit, that first or later may bite him in the neck.

Also, I would throw a defined in there for one may well want to replace say <?--cost--> with 0.