Flash is almost a must. There will be many cases where you will have placed a time bomb on an enemy with low health, and they run back. Flash, bomb, boom!

For those of you who prefer exhaust or other slows, let me bring you to case 2 for choosing flash. You have just been ganked 5v1 by the other team. You run to a barrier in your final second, and cast crono on yourself. They kill you. You revive. You immediately flash over the wall, haste yourself, and run off laughing.
Ignite is quite nice, mainly for the 10 extra early game AP. This turns out to be quite the boon, as you are constantly CONSTANTLY bombing them. 9 extra damage per bomb adds up over time. The healing reduction is also nice, it prevents irritating last second heals before your bombs go off.
I have used cleanse some to further infuriate people who try and gank Zil, but it hasn't been as effective as others. If you're going to be more of a support/tank, it is worthwhile considering a 9/21/0 Mastery build picking up both cleanse and fortify.
Clairvoyance: If you get it in solo queue, it will be wasted. People won't call for it, they'll say it is useless... However, in arranged games where you communicate, (either over Ventrilo or in chat more) clairvoyance can be very useful. Unlike Teleport, Ghost, and Revive, Clairvoyance takes time to master and use efficiently. If you have already used it well before, go ahead and get it!

Spells not to get:

Clarity: In my build you will have a chalice. Late game, you should have golem buff most of the time. Early game, the +7m/5s will be more than enough and should tide you over until your first trip back.

Ghost: You already have the same effect on a skill with far lower CD. No use, really.

Teleport: I have never found it too useful considering you have a MS of around 500 permanently late game.

Heal/Revive: Does anybody still take this skill anymore? Zil has enough range that he can avoid being harassed too much fairly easily. Lategame, the amount healed is not too noteworthy.
And as for revive.... 0.o Haven't seen this one used since level 3. Pretty useless.

ALWAYS:
1)Bomb
2)Rewind
3)Bomb
4)Time Warp
5)Bomb
6)Crono
7)Bomb

Taking bombs whenever possible does not need an explanation. It's a nuke that also devastates creep waves once you've got some AP. Truly a great skill.

Rewind at level 2 allows you a great chance of pulling off first blood at level 3 or so. A double time bomb at level 3 (along with ignite or general ally help) will always scare the enemy to death, hopefully literally.
In late game, think about rewinding even if only your ult is on cooldown; you probably have the mana to spare - especially once you get the golem buff.

Did you know if you time warp an ally, and they get the kill, you are counted as assisting them? Important information once you buy soulstealer.

Finally, Chrono. The ability that will cause the most tears and ragequits on the enemy team. Especially in 1v1 battles with Zil, where they just "killed" you and you come back from the dead and bomb them into the ground.
To me, Crono is like a buffed-up version of Tryn's endless rage. For 15 seconds, you are essentially untargetable - if they kill you, presto! You're alive again, and, because you followed my advice, you can flash and time warp away. If they don't kill you, then, well, they don't kill you. You survive. Hooray.

If a hero will die in the next fifteen seconds, use it. But if there are multiple heros who will probably die, you have a choice. Which one is most likely to die? Which one will die first?
Make sure to use this on heros that take an additional penalty from being killed, or have especially good escape mechanisms.
Case 1) Cho losing his feast stacks.
Case 2) Anybody losing one of the 20 stacks. (Soulstealer, Leviathan...)
Case 3) Natural blinkers/dashers. (Ezrael, Shen, others)
Case 4) People who have large crowd control effects/disrupts that they haven't used yet (Nunu, Amumu, Janna, others)
Or, in short, pretty much any hero.
Note: If you are going into a teamfight, you should make sure you have enough mana to do both Bomb-rewind-bomb and Chrono. It is not fun to go, "Bomb-rewind-bomb-oh**** I don't have the mana for Chrono"


After level 7, it no longer matters as much which skills you take. I tend to take both evenly, and perhaps pushing rewind a bit more if I'm having a good game and getting tons of charges on Soulstealer.