If you're in Hypermode, a 40% EXP boost applies. [Wiki]
If today's V-Wave Type matches that of your Egg/Pokémon, a 50% EXP boost applies. [Wiki]
If you're the PokéRus host, you get twice the EXP boost. [Wiki]
Users with the Wiki Editor rank get a 10% EXP bonus. [Wiki]
Users with the Helping Hand rank get a 10% EXP bonus. [Wiki]
You get 30% bonus EXP on the week of your birthday! [Wiki]
There's a Fossil Pokémon in your party. This boosts Eggs of the same Pokémon with twice the EXP. [Wiki]
Discord Nitro users get a 10% EXP bonus for boosting the PFQ server. [announcement on the Discord server]
A normal day gives x1 EXP. Change this number when Niet's Counter is active. Multiples of .5 are also accepted. [Wiki]
Your Eggs get bonus EXP depending on how many Pokémon of the same evolution line you have in your Party. [Minor Updates, 11/May/2015]
Select the Badge Level applied to your Egg's Type. For dual-Type Eggs, select the highest of the two. [Wiki]
EXP gained per click:
Egg EXP Clicks