I'm gutted that NZBMatrix has gone, I liked the way they categorised everything and no other NZB indexer does. There are other indexers still going, like NZBIndex.nl.
I use Newsleechersoftware which used to have an annual subscription, including an option for a 'Supersearch' feature that allows you to search across all newsgroups. It seems they've got rid of that though in favour of a monthly subscription which I'm guessing I'll have to switch to when my current subscription expires. The monthly subscription is $4, including Supersearch.
It's the most rated indexing site at the moment. I have noticed that a lot of the content indexed is unavailable, so this could indeed be the beginning of the end. Was bound to happen eventually I suppose.