- I run ignite vs high sustain / healing laners. I'll take  over ignite most of the time for better map control. Elise has an easy time killing people that have low health, so by using your E in spider form more effectively, you should be able to get another Q on someone that is in kill range regardless of flash.

 - Flash is a must have for Elise. It can boost the range on her Q in spider form to finish off a runner, as well as aid her escape mechanic if there isn't any minions near by to Rappel to. 

 - Ghost is a good choice if you substitute any Movement speed for Pen

The movement speed quints are necessary. She needs to be able to keep up with someone, as well as dance and harass with her Q range. When her W is activated in Spider form, you need to be able to stay in melee range to effectively out sustain and tank. 

Armor and Magic resistance to help maintain safe trades that QUICKLY snowball in Elise' favor. Since your Q does a percentage enemy health (total health in human / missing health in spider).

Attack speed helps take advantage of Elise' spider form sustain with W. It goes hand in hand with  as far as reaching maximum stacks in Human form while still harassing with Q. 

The defensive tree can be switched around to better suit her lane. for example I may take minion defense if I'm going into the jungle, or all MR if I'm going mid vs an AP burst.

Knowing who your laning against can give you a huge advantage. Specially if the other team can't guess where you'll be. Since Elise does well Top / Mid / Jungle, you have a lot of options with the last 9 points. Although since the recent changes in the mastery trees for season 3, I feel that Utility masteries don't become beneficial till a little deeper in.

These masteries go hand in hand with my build / runepage. Attack speed reds, and flurry stack, while skipping over the measly 4% cdr. 18 AP at 18 for the next trait giving Elise about 1/3 of her needed AP to scale into late game naturally. Havoc works beautifully since it increases Elise' over all dmg regardless of the source, and arcane knowledge for early game PEN for harassment! (Now do you see where I'm going? :) ) Mental Force and spellsword continue to increase Elise' dmg without sacrificing any stats that she doesn't need. Archmage increases her AP again to scale naturally into late game without having to waste a ton of money on heavy AP offensive items that don't really scale well for Elise. Executioner being an obvious choice for stacking with your Spider form Q.

Elise gets a HUGE defensive bonus when she switches to spider form, I found enhancing this natural tanky ability with masteries was way more beneficial than going down the utility tree. IMO the utility tree doesn't start getting good till the 3rd tier in and still requires a heavy investment. If you're in a top lane (which you probably will be due to the fact that you win MOST top matchups) You probably aren't getting blue buff anyways, personally don't think you need it either but it does help keep harass up and mana to stay in lane, making Runic Affinity next to useless.

Going down the defensive tree allows you to customize your defenses to better suit your enviroment. If you're going top vs a melee AD with a weak early game you can REALLY take advantage of how strong you are early SPECIALLY at melee range. If you're going mid you can stack your MR to take reduced damage from their spells. Even if you have a prefered Elise jungle set up, you can move the defensive tree to take less damage from minions and even return some if you'd like. 

 - "With thise rune / Mastery combo, no one can stand up to me and my children! -MUAHAHAHAHHA-"

Spider form E is a 1 point wonder, but it can be difficult to land if your opponent is ready for it. Since your E is on such a high cool down, it is usually the deciding factor in you being killed, or getting a kill. 

NOTE: Your rappel is a WONDERFUL way to mitigate damage you know is coming. IE Ziggs ult, skill shots, aoe etc. You can use this when you initiate to trick the team into burning a large portion of their spells. I warn you though, if they catch on to you, they will be waiting!

W is generally maxed 2nd for damage, however in the event you find yourself in the jungle, I find putting 2 points into W before maxing Q helps her stay sustained in the jungle as well as clearing jungle creep. If you still feel like you're getting your ass kicked, you can max w and build more attack speed and you'll do just as fine because the scaling on her q is so low. 

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RAPPEL DOES NOT STOP DOT DAMAGE. THIS INCLUDES .

Since Elise is strong on her own, her build can be customized to directly counter your opponent.

 

Elise's AP scales VERY poorly, she benefits much more by taking advantage of her natural tankyiness and the insane dmg increase/sustain on her Spider form W.

By taking advantage of Spider form W, coupled with core item , you can tear down ANYONE. Malady allows Elise to directly build into her core dmg stats without sacrificing gold on a stat that doesn't benefit her. MR  debuffs on every auto attack mean your final Q will be enough to finish the job. 

 Liandry's Torment also gives her ALL the pen and AP she could ever ask for freeing up TONS of defensive item space without sacrificing any damage. NOT TO MENTION THE PASSIVE INCREASES HER DAMAGE WITH BOTH AD AND AP DEFENSIVE ITEMS!!! THIS IS SO IMPORTANT (/)

With Season 3 masteries and runes, Elise becomes much tankier / faster / and stronger without having to sacrifice damage. Elise does large amounts of damage with low AP numbers.