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It doesn't work! I activated the plugin but I can't see the reply links.

They should be visible only when you move your mouse cursor over a comment text. If it still doesn't work, open at-reply.php search for visibility:hidden; (line 26) and remove that part, then you can also remove the whole line 29 li:hover .yarr { visibility:visible } because it becomes useless. This will make the reply links always visible for all comments (and not just the one your mouse cursor is over).

It doesn't work! I can see the reply links but clicking them does nothing.

Either you have disabled JavaScript in your browser or your WordPress theme is not using the default id for the comments textarea (which is comment). In the later case, check your comments.php file to find your textarea id, then open at-reply.php and replace all the document.getElementById('comment') with document.getElementById('YOUR_ID').

This version sucks! I prefer the old one because I could choose where I want to put the reply link.

It's hard to please everyone. For me, @ Reply should be a built-in theme feature and not a plugin. But plugins are easier to install (when it works). You can still download the previous version, just remember to replace Version: 1.0.1 with Version: 2.8 (or any higher number) on line 6 so that WordPress doesn't suggest you to update the plugin.

Possible conflicts with other plugins.

A plugin that filters the default WordPress comments functions, may prevent @ Reply from working. For example, WP_Identicon does this, but it also has an alternate setup for "advanced users" that doesn't conflict with @ Reply.