Other than the big names already mentioned,
Short Beaks Ltd do good deals under their 'special offers' menu from the home page. Just chose Ghent as an example. Not really last minute specialists, although it might be worth calling them if there is nothing available according to the website. I can't think of any others.
Personally, I would just book train tickets onilne and take a chance on arrival, or pre-book hotels online also at this time of year, rather than go with a package. Paris is always going to be pricey for accommodation last thing unless you get lucky, or have particularly good negotiating skills, but all the smaller cities like Ghent, Lille, Bruges, Leuven, Antwerp etc should be easy enough to find a double room for Two nights for less than €100 on arrival. Often, it can be the more luxurious 3 star places offering better 'on the night' deals.
I don't have the same restrictions most people do. Also, I consider any long train ride on a nice train a holiday in itself. Don't think I have advance booked a train for over 15 years. Just turn up at the station, ask for the cheapest option on the next available train. That may mean a 6 hour wait (or, longer), and often means paying around 30% more compared to booking just Three days earlier. Late night arrival in a strange city can make finding affordable rooms a bit stressful mind. Other than holiday weekends etc, I wouldn't expect finding reasonable prices on the day a problem.
