First of all, which version of WordPress are you using? Make sure it is the latest version available from the DOWNLOAD link at the top of this screen. The spam fighting tools are amazing that come built in.
Second, try two of the best comment spam fighting tools. Bad Behavior and Spam Karma 2. Both of these plugins will put an end to your comment spam woes.
In other words – put back the core template files that you removed unwittingly and give these a try.
To totally turn off comments, then in your Administration Panel, go to Options > Discussion and turn off comments there.
I have several websites all using Bad Behavior (BB) and a couple using Spam Karma 2 and I have little or no problems with spam and these are heavy traffic sites.
For more information, see Fighting Comment Spam in the WordPress Codex.
I’m actually having somewhat of a similar problem, only I have commenting enabled for anyone, without moderation or any sort of restrictions and yet I’m still getting comments being held for moderation. Any help on why this is happening and/or how to fix it (preferrably how to fix it, at least)?
Do the comments that are getting held for moderation have more than the allowed number of links? (This is set in Discussion options, just over the moderation and blacklists. Default is 2.)
they don’t have links at all, actually. There’s nothing in the blacklists either.