The process of 'spending' skillpoints is hugely different from regular training, and I've seen a bunch of pilots just applying it to whatever skill they're currently training. Considering that many of these players are the kinds to optimize and tweak skill plans in EveMon I find it quite surprising that the same amount of effort wasn't applied to the skillpoint decision.
The ideal strategy is to spend it on the skills which you learn slowest, and for most people that means anything with Charisma as a primary attribute, so, put points into those Trade, Social, Leadership and even Planetary Management skills. You may not have been planning to learn those right now, but you'll save yourself a few hours down the road. And should you have been lucky enough to get this bonus while you were still inside your <1,600,000
Myself, I realised I could put a couple of levels into negotiation, and get some extra points in leadership. Meanwhile my training towards large Hybrids V is almost over.