Not all may know that you retain your positive promotions as you upgrade your units. A lot of unique units have some nice bonuses right off the gate and if you manage to keep them alive until you reach the needed tech for the upgrade it will pay off quite nicely. As upgrading old units seems to be the way to go in CiV anyway it would be wise know your options. I have listed all the unique units' bonuses here for you convenience and my opinions of them.
Really good bonuses. These are good enough to base your strategy around:
Jaguar Combat bonus in Jungle only (50) + heals 2 damage if kills a unit Upgrades to swordsman
Because Jaguar comes so early you can really benefit from its bonuses. Jungle combat may be rare but its something to keep in mind if situation arises and kill-healing will keep your Jags alive and operational.
Janissary Heal if destroy enemy (non-barbarian) + Combat bonus when attacking (25) Upgrades to rifleman
These bonuses are just ridiculously good. Too bad nothing upgrades to musketman and they become obsolete so quickly. It is still worth avoiding rifling until you can build a nice Janissary force and then benefit from super powered gunpowder units for the rest of the game. As a matter of fact that might be the only reason to play Ottomans at the moment.
Cho-Ko-Nu May attack twice Upgrades to rifleman
China's UU is already good and if you plan ahead you can get really high powered riflemen later. Cho-Ko-Nus get experience almost twice as fast as other units because they gain xp from every attack. You can set up a nice xp farm from a city state and bombard it and its units with Chokos and retreat to heal when necessary. Honor trees double experience will help obviously too. Or you can use them in actual conquest too as they are really good units on their own right. Just remember that it is not wise to actually promote your archers as ranged promotions do nothing once you upgrade to rifleman. But when you finally do you will get really powerful units for the rest of the game. Blitz is not necessary as you can already attack twice a turn but small band of marching medics is nearly invulnerable if you don't get too reckless.
Samurai Shock I + Great generals II Upgrades to rifleman
Just all around goodness. You obviously want to go iron route and avoid shock promotion for earlier units as you will get it with Samurais.
Average bonuses. These nice to have but not that powerful imo:
Mandekalu Cavalry Bonus vs cities (30) Upgrades to Cavalry
Bonus is nice but I'm hesitant to go Cavalry route as they will become useless later in the game as they are upgrade dead end. Still might be worth it if you can manage to get a decisive lead with cavalry warfare.
Foreign legion Combat bonus outside friendly territory (20) Upgrades to mechanized infantry
Solid bonus that comes a bit late. Still nice to have.
Companion cavalry Great generals I Upgrades to Knight
Bonus is not that great but since you are building companion cavalries anyway it is a icing on the cake.
Naresuans Elephant Bonus vs mounted (50) Upgrades to Cavalry
Same as songhais unit exept the bonus will not matter as much.
Mohawk warrior Combat bonus in forest/jungle (50) Upgrades to longswordman
Nice bonus but AIs tend to chop their forests away so it might not matter much later in the game.
Immortal Heal at double rate Upgrades to Pikeman
Solid bonus but it takes imo quite long to reach rifling and you want to ask yourself do you want to pay upkeep for nearly useless (for some time) pikemen until you can upgrade them to riflemen.
Minuteman All tiles cost 1 move Upgrades to rifleman
This ability can be a liability as you cant use your own roads but it can pay off later when you can blitzkrieg with mech infantry.
Minuscule bonuses. Says it all really:
Landsknecht Bonus vs mounted (100) Upgrades to rifleman
Not really a special ability as pikemen have it too but can sometimes come to play if your rifles go against knights or cavalry. Again is it worth to pay the upkeep until the upgrade though?
Zero Bonus vs fighters Upgrades to Jet fighter
Like this would ever matter.
Ship of the line- Extra sight (1) Upgrades to destroyer
A tiny boost but nothing to write home about. Note that caravels also have extra sight that they retain when upgraded to destroyers.
Really good bonuses. These are good enough to base your strategy around:
Jaguar Combat bonus in Jungle only (50) + heals 2 damage if kills a unit Upgrades to swordsman
Because Jaguar comes so early you can really benefit from its bonuses. Jungle combat may be rare but its something to keep in mind if situation arises and kill-healing will keep your Jags alive and operational.
Janissary Heal if destroy enemy (non-barbarian) + Combat bonus when attacking (25) Upgrades to rifleman
These bonuses are just ridiculously good. Too bad nothing upgrades to musketman and they become obsolete so quickly. It is still worth avoiding rifling until you can build a nice Janissary force and then benefit from super powered gunpowder units for the rest of the game. As a matter of fact that might be the only reason to play Ottomans at the moment.
Cho-Ko-Nu May attack twice Upgrades to rifleman
China's UU is already good and if you plan ahead you can get really high powered riflemen later. Cho-Ko-Nus get experience almost twice as fast as other units because they gain xp from every attack. You can set up a nice xp farm from a city state and bombard it and its units with Chokos and retreat to heal when necessary. Honor trees double experience will help obviously too. Or you can use them in actual conquest too as they are really good units on their own right. Just remember that it is not wise to actually promote your archers as ranged promotions do nothing once you upgrade to rifleman. But when you finally do you will get really powerful units for the rest of the game. Blitz is not necessary as you can already attack twice a turn but small band of marching medics is nearly invulnerable if you don't get too reckless.
Samurai Shock I + Great generals II Upgrades to rifleman
Just all around goodness. You obviously want to go iron route and avoid shock promotion for earlier units as you will get it with Samurais.
Average bonuses. These nice to have but not that powerful imo:
Mandekalu Cavalry Bonus vs cities (30) Upgrades to Cavalry
Bonus is nice but I'm hesitant to go Cavalry route as they will become useless later in the game as they are upgrade dead end. Still might be worth it if you can manage to get a decisive lead with cavalry warfare.
Foreign legion Combat bonus outside friendly territory (20) Upgrades to mechanized infantry
Solid bonus that comes a bit late. Still nice to have.
Companion cavalry Great generals I Upgrades to Knight
Bonus is not that great but since you are building companion cavalries anyway it is a icing on the cake.
Naresuans Elephant Bonus vs mounted (50) Upgrades to Cavalry
Same as songhais unit exept the bonus will not matter as much.
Mohawk warrior Combat bonus in forest/jungle (50) Upgrades to longswordman
Nice bonus but AIs tend to chop their forests away so it might not matter much later in the game.
Immortal Heal at double rate Upgrades to Pikeman
Solid bonus but it takes imo quite long to reach rifling and you want to ask yourself do you want to pay upkeep for nearly useless (for some time) pikemen until you can upgrade them to riflemen.
Minuteman All tiles cost 1 move Upgrades to rifleman
This ability can be a liability as you cant use your own roads but it can pay off later when you can blitzkrieg with mech infantry.
Minuscule bonuses. Says it all really:
Landsknecht Bonus vs mounted (100) Upgrades to rifleman
Not really a special ability as pikemen have it too but can sometimes come to play if your rifles go against knights or cavalry. Again is it worth to pay the upkeep until the upgrade though?
Zero Bonus vs fighters Upgrades to Jet fighter
Like this would ever matter.
Ship of the line- Extra sight (1) Upgrades to destroyer
A tiny boost but nothing to write home about. Note that caravels also have extra sight that they retain when upgraded to destroyers.