I'll just make a short list of some ideas, don't have the proper time to write some big entry as I normally do and most people don't read text walls anyway. :/
1st: Mortars.
Using the old effects with the new effects' colors and explosion.
Or even make faction-mortars with the old effects, recolored for every faction that has mortars?*
2nd: Primaries and secondaries
Using the vanilla effects for the primaries. Somehow they just had a nostalgic feel to them. I miss them, to be honest. The new effects are nice and all, but just not as Freelancer'ish.
3rd: Cerberus / Heavies
Using the new Primary turret projectile effects for new faction "Cerberus" / Heavy turrets instead.
* In vanilla guns had an effect template and would just be recolored by an .ini file (beam_effects.ini) as I understand it. Maybe such would be possible for that as well?
(Heh, maybe I'm just a nostalgic, but such small stuff slowly takes away from the vanilla feeling for a cap-lover...)