I need to make a last minute travel. Its not optional, and last minute means I have one hour to book it and will be flying next day. I need to fly within Europe. Is there a fare search engine that specializes in this? Are there other options?
There's no special system for sub-1 hour travel. It's the same search algorithm, and the same rules. In that sense, use your usual favourites.
However, there is a big difference: you may find that many online travel agents will be reluctant to issue a ticket at less than one hour to departure: it leaves them with little time to sort out any problems if the ticket needs to be manually issued or if there is a payment problem.
Therefore I suggest going straight to the carriers' websites and checking there. If you know you have one hour you probably already know which flight you want. So it is really a case of checking on the carrier's site, and any major codeshare partners.
You should also be aware that many carriers will close their online check in at about 1 hour prior to departure and close the desk check in within a few minutes after that. So you do not typically have a lot of time to be worried about saving 50 Euros here or there. Your main worry with this kind of last minute travel is actually getting the ticket issued and checked in before the deadline.