Classes and Prestige Classes
Things to look out for when choosing your class:
Spell Progression: If your class has a delayed progression, you will probably be missing out on 3rd level spells.
Hit Die: Hit Dice actually matter quite a bit in E6, as you not only are lacking the better defensive options from high levels, you are also fighting things that likely have a higher attack bonus than you can keep up with.
BAB: If you are a martial character, (almost)never go under 6 BAB. That extra attack is almost always better than what you are getting for that low-bab dip.
Prestige Requirements: Most prestige classes intentionally limit you from entering until you are already level 5, making PrC dips a capstone of sorts. Early entry tricks are a good way around this, but your DM may start throwing books at you when you start going Wizard1/Shadowcraft Mage5.
Acceptable Items in the setting:
This is the one thing that needs to be addressed. You're practically tying players hands if you limit it to what 3rd level spells can create. At the same time there are plenty of items with low requirements that don't fit the system at all. I find that limiting the max value of an item to 10,000gp to 11,000gp to be a decent enough solution. It allows for +2 weapons and +3 armors as well as +2 max stat boosting items.
Artificer:Many DMs outright ban this class in E6, due to the uncapped potential and the access to spells. It has the (debatable) ability to craft items that require 4th level spells, including scrolls of said spells. A sane DM that still wants to allow the class would be advised to cap the spell access at 3rd level spells and use Unearthed Arcana's Craft Points to streamline the class so as not to cause as many issues.
Factotum is unique in the system as it is hands down the best team player. It can be gestalted with nearly every class to yield good results.
Passive Classes such as Dragon Shaman or Marshal are also very good choices for Gestalt.
