Note upfront, for clarity: ships in EVE enter warp at the ends of the server's 1 hz ticks, i.e. at the end of every clock second.
Here's a decent overview of warp mechanics, and I cover it in bullet #2 of the dropdown "essential knowledge" section of my intro guide.
These factors affect Time to Warp (hereafter TTW):

• mass
• velocity
• direction relative to point of warp
• intertia modifier, commonly called agility
• collisions (or lack thereof)

For the purposes of entering warp from a dead stop, an align time of 2.01 s is the same as one of 2.99 s; they'll both enter warp on the 3rd tick.
Align time is not the only reason to be concerned with ship mass & inertia, though, since nimbler ships also accelerate and turn faster during combat.

These skills may decrease TTW:

• Evasive Maneuvering improves agility for all ships
• Spaceship Command improves agility for all ships
• Advanced Spaceship Command improves agility for all ships requiring the skill (freighters, jump freighters and capitals)
• Armor Layering reduces the mass added to hulls by armor plates, thus marginally reducing their TTW if such plates are onlined
• Advanced Armor Layering further reduces the mass added to hulls by armor plates
• Amarr Hauler improves agility for the Sigil
• Caldari Hauler improves agility for the Badger
• Gallente Hauler improves agility for the Nereus
• Minmatar Hauler improves agility for the Wreathe
• ORE Freighter improves agility for the Bowhead

These fittings may decrease TTW:

• Inertial Stabilizers (low slot)
• Nanofiber Internal Structure (low slot, less agility boost than istabs but with no sig radius bloom; also increases subwarp speed)
• Low Friction Nozzle Joints (rig slot)
• Polycarbon Engine Housing (rig slot, less agility boost than nozzle joints but also increases subwarp speed)

These drugs may decrease TTW:

• Quafe Zero Green Apple - given out during events and as Twitch drops
• Halcyon G-[X] - these were once given out as random login rewards, but not anymore. other Halcyon boosters have been given as Twitch drops
• AIR Agility Booster II - one of these account-bound drugs is given out to any character that jumps 100 stargates as part of the AIR Career Program
• limited-time agility-enhancing drugs are sometimes available during events (these are different than QZGA, which does not expire)

These implants may decrease TTW:

• Eifyr and Co. 'Rogue' Evasive Maneuvering EM-70x hardwirings (where x = 1-6)
• Nomad attribute enhancer sets - see Steve Ronuken's handy list of current prices for all implant sets

The Evasive Maneuvering Command Burst charge may decrease TTW, however:

• Command Burst use gives the activating ship a weapons timer, preventing stargate or Ansiblex jumps for 60 seconds
• Command Burst bonuses are temporary, lasting 60-135 seconds, and do not persist across stargate, Ansiblex, or wormhole jumps

These fittings may increase or decrease TTW, depending upon the situation:

• afterburners and microwarpdrives (mid slot, only if active, also increases mass a good bit, so pay attention if using wormholes)
  • whether they increase or decrease TTW depends on the lengthafterburner cycle length is reduced by the Afterburner skill
    and increased by the Zor's Custom Navigation Link implant of their cycles, when they are activated relative to warp initiation, and the hull's current inertia modifier and mass
    • for instance, if a battleship fit takes 13.1 seconds to align, turning an MWD or AB on & off immediately after warping will decrease its TTW from 14TTW is always rounded up to a whole second seconds to 10, 9, or 8
    • by contrast, if one initiates warp in that same battleship then waits and activates an MWD/AB at ~60% of max velocity, TTW will increase
    • there are also more advanced things you can do, like scram-webbing a super/titan into warp, or doing that with a non-supercapital ship if you're good at timing & positioning
• Higgs Anchor (rig slot, also dramatically increases mass, so pay attention if using wormholes)

The Statis Webification effect may:

1. have no effect on TTW: if you're at a dead stop, being (continuously) webbed doesn't alter TTW
2. increase TTW: if you're being webbed and don't have 75% max velocity towards your warp vector, TTW increases if the webbing stops (because you must accelerate yet more)
3. decrease TTW: if you're unwebbed and have ~1-35% of max velocity before being webbed, you'll enter warp instantly on being webbed
   • the exact speed at which any given hull can be "webbed into warp" depends on the hull & fit, the pilot's skills/drugs/implants, and the strength of the web effect(s)
   • the effect can be applied by ship-mounted grapplers, webifiers or web bursts, or by structure-mounted webifiers or web bursts

Armor plate modules may increase TTW by adding mass to hulls (low slot, only if online, pay attention if using wormholes with plates fitted)

• whether they'll actually cause a ship to jump up to a longer align breakpoint depends on the mass of the ship & other stuff like all the above

The Black Hole system effect effect may increase TTW:

• certain J-Space (JS)Systems whose names all start with the letter J, accessible only via wormholes (2,603 total). systems have an effect which, among other things, increases the inertia of all ships inside, thereby increasing their TTW