There are many bonuses which are commonly suggested for new civs/civ ideas (e.g. free archer line upgrades, buildings regenerate slowly, smaller farms etc.). Here are a few which are less commonly suggested. Some of these would be the "main bonus" of the civ, some could be a team bonus, and some would be a bonus thrown in to round things out.

An interesting list of civs (and civ bonuses) can be found in this page which describes the "realms" mod for AoE2.

Economy

• the first of each building you build returns 50% of its cost (excludes buildings which cost stone)

e.g. the first mill you build returns 50 wood when it's completed; siege workshop, 100 wood etc.

• starting in the castle age, town centres spawn a sheep every 170 seconds

170 seconds is roughly the time it would take 1 villager to harvest 1 sheep

• fishing ships carry 5 more food and build fish traps 100% faster

• fishing ships gather from fishing traps 15/20/25% faster in fedual/castle/imperial age and fishing traps have +285 food

• start game with the 15 tile aoe around your TC explored (but not visible)

• start game with the 15 tile aoe at each corner explored (but not visible)

i.e. equivalent to an outpost with 15 LoS placed in each corner and then deleted. good for scouting where to put trade as well as resources.

• (UT/unique building) Gain permanent vision over the corners of the map (20 LoS)

to spy on enemy trade etc.

• +10 population per age (starting in dark age)

i.e. "2 free houses" per age

• +1 population every 60 seconds

i.e. "1 free house" every 5 minutes

• in imperial age, once crop rotation is researched, farms provide unlimited food

i.e. crop rotation changes from "+175 food" to "+9999999 food" (or whatever). farms still cost 75 wood to build. farms built before the tech still need to be reseeded.

• from castle age, while you have less than 200 of a resource you gain a slow trickle of that resource (these values are doubled upon reaching imperial age: 30 wood/minute; 30 food/minute; 15 gold/minute; 7.5 stone/minute)

Research and techs

• buildings (except stone walls, watch towers, TCs, castles, and wonders) can be built 1 age earlier.

this does not alter prerequisites for buildings (you need a baracks for a stable), units (feudal age is needed for scouts), or techs (2 dark age buildings are needed for the feudal age tech; feudal age is needed for fletching)

• techs (excluding age up techs) research instantly, but have a delay before they "kick in" (the delay is equal to their research time)

some examples: you can research loom and produce a vil at the same time. you have to wait for fletching to kick in before researching bodkin. you can research archer armour and fletching at the same time.

• all blacksmith techs are free 10 minutes after advancing to the age.

e.g. all feudal blacksmith upgrades are free 10 minutes after feudal age is reached. nothing happens if the tech has already been researched.

• (team bonus) scale mail armour is free in dark age.

• archers benefit from barracks techs

tracking, arson, squires. +2 LoS; +2 bonus damage vs standard buildings; +10% speed.

Misc.

• units always deal at least 3 damage

done by subtracting 3 damage from the unit's attack and adding 3 bonus damage (against all units, using an unused armour class). (may have unintended consequences (e.g. galleon doing 7 damage to a battering ram instead of 4))

• houses +50% hp; +1/1 armour; +4 line of sight

• (Unique building) Healing shrine: size: 2x2; HP: 1800; healing range: 10; max units healed: 3; healing rate:1hp/0.4s; cost:150w 200g

• (UT) town centres +3 range, +2 damage, +2/2 armour

• free monk on reaching castle age

• farms and fish traps have +200% hp