I generally indent as follows:

if ($x) {
    if ($y) {
        code;
    }
    code;
}
else {
    code;
}
[download]

Though some smaller bits of code can be formatted like this:

if ($x) { code; }
[download]

Or even this (since this is Perl):

code if $x;

long section of code
    if long test on $x;
[download]

The style of indenting depends primarily on the size of the blocks, imho, though there are some indenting methods I hate:

if ($x)
    {
    code;
    }

if ($x)
    { code; }
[download]

Etc. The former produces far too much white space; the latter makes for some real problems lining things up.