I guess everyone can chalk it up to their own personal experiences but I've noticed a great many differences between 1.6 and Source. Now the develepors deny the existance of some of these, but it's fairly obvious they are there.
Movement --
1.6 : It seems unrestricted save for jumping.
Source : It seems like you have to shift your weight around when you change directions sometimes.
Recoil --
The developers deny any difference with recoil but I think we all know it's there.
1.6 : Spray is not too effective at long and medium ranges. Burst shots are your best bet.
Source : Say what you will, I can pop a guy in the face at long range consistently with spray, while in motion. It just gets ridiculous sometimes.
Hitboxes --
1.6 : Hitboxes came a tad off the model. Possible to get a headshot when you were aiming slightly above the head.
Source : Seemed that the hitboxes lagged behind the player. Shooting behind where he is would score you a kill (helps with the spray argument).
Weapon delays --
1.6 : Slight pause before you can fire, nothing so bad that it will get you killed.
Source : A slightly longer pause it would seem most of the time. Can get you killed in the middle of an intense firefight.
Grenades --
1.6 : No mass to the grenades, they fly around easily and are easily seen due to a very visible size. Can bounce them around corners pretty far. Flashbangs only blind, no hearing loss. HE grenades cause damage through walls, no hearing loss. Smoke grenades are fairly easy to see through.
Source : They seem heavier and fly on a lower angle. Are far smaller and harder to spot. In fact you can even damage a person by throwing a grenade at them. Harder to throw grenades off of walls. Flashbangs and HE grenades cause hearing loss. HE grenades no longer damage through walls. Smoke grenades are very hard to see through.
Animations --
1.6 : Basic animations for what have you, decent enough. Player models seem to be standing upright. A nice kill animation if you get shot with something powerfull (fly back) or a headshot (fall backward).
Source : Basic animations are just as nice. Player models seem to be hunchbacked. Ragdoll is a definite plus most of the time. Headshots no longer make the player fall backward, powerfull shots no longer push the player back.
Environment --
1.6 : Save for planting the bomb or breaking glass, nothing really going on here.
Source : Canisters, picture frames, computers, planks, etc etc. Very nice interactive environment.
Walling --
1.6 : Can shoot through various walls and objects. An advanced tactic used when you know where someone is but don't have a line of sight.
Source : Bullets no longer travel through anything except a few select things. Not very usefull at all.
Obviously I'm not going to compare graphics because that's what Source is all about. Weapons, maps and models are also moot due to Source having (or going to have) all the same.
Source has a lot of good points, but it also has some bad. Overall gameplay I would say 1.6 still has it over Source. Patches will come, Source will get better and then it will overtake 1.6, but not as it stands now.