My Preference (inferred by play time) goes in this order:
Medic > Solidier > Heavy > Sniper > Engineer > Pyro > Scout > Spy > Demoman.
In the original (and to an extent TFC), my favored order was probably (I have no stats to back it up)
Pryo > Spy > Medic > Sniper > Engineer > Soldier > Demoman > Scout > Heavy.
I really miss the grappling hook, dirty syringe, incendary rocket launcher and MIRV grenades, but the changes seem to have been for the better (I generally seem to get killed on purpose rather than as an unintended side effect of MIRV spam - which put most forms of video game spam to shame).
Most of the order changes came as a result of game changes. The Pyro's emphasis on brutal point blank firepower versus mid ranged annoying lethal firepower moved that class down the list. The increased utility of the medic from a pure healing perspective moved it up on the list (the difference between success and failure seems to often be based around how competent your medics are). The spy just operates on a totally different feel these days (though the spirit of the system is still there), and I might not have given the class a fair shake. The Heavy's ability to move and shoot (plus the medic sidekick) means the heavy is no longer that "impromptu door" from the old days moving him up a great deal. Engineer is just as useful as always, but I don't like babysitting sentries (but someone's got to do it). Soldier is just as lethal as ever but high speed internet (I was on 28.8k for TF) means I can better apply said firepower. Finally, I've always been a terrible demoman, but I have to say the demo is probably the most lethal class in the game in skilled hands (and it seems always has been).