1) Action Economy Is Still King
-Full Triple-progression casting is cute, but ultimately futile in combat since nearly every spell, Power, Invocation, etc takes a Standard Action to use, and you still only get one of those per round. Try to mix your activation abilities up, between Standard, Move, and Swift actions, so that you can get more out of what you have.
2) Focus On One Theme
-Having schizophrenic capabilities just means you'll be more at a loss in combat, despite the increased options, especially if the two sides interfere with each other in normal use. Barbarian/Wizard, though it may sound awesome, generally either gives up most of the benefits from one side of the progression or else is just confused in battle. If it can't be effectively done on one class, it generally isn't worth doing on two.
3) Strengthen Each Other's Weaknesses
-Since you always take the higher HP, BAB, Save, skill points and both skill lists, try to ensure that your secondary class is good at some things that your main one isn't.
4) Remember Your Stats
-Twice as many "classes" means twice as many opportunities for MAD. Make sure your key abilities from both sides are still lined up onto one or two main stats
5) Remember Your Feats
-Feats are the one thing you don't get multiples or increased numbers of normally. This makes prerequisites and feat chains just as hard to squeeze in as normal, more so if you want to Prestige on both sides of the equation (and many do)
6) Dipping Is Easier
-In Gestalt, dipping 1-3 levels on one side for supporting capabilities does not delay or prevent high-level capabilities from your other side. Ftr 2 for feats and proficiencies, Paladin 2-3 for Cha to saves and immunities, Meldshaper levels, etc are all simple and powerful options.
7) Beware Wasting Identical Advantages
-This causes pure waste. A PrC attempting to increase your Wizard caster level on one side and a level of Wizard on the other just lost a caster level benefit. Similar things go for other benefits, such as Uncanny Dodge, high HP/skills, and Proficiencies (not as much a concern as the others).
8) Active/Passive Mix is Typically Best
-Let one side have the abilities which require actions. You can put together cool utility, long-term buffing, bonus feats, and static/reactive abilities on the other side
9) The Very Worst Classes Sometimes Aren't Bad Here
-Monk, with its dominant saves, decent skills, and host of static abilities, is a FAR better choice for support-side levels than it is for single-class. The Expert, despite being an NPC class, notably is able to pick ANY TEN SKILLS as class skills with 6+Int per level, which can be clutch if your prereqs are getting tight. Any class that usually has the phrase "if only it had ___" can easily acquire it. Basically, almost anything can be of benefit to SOMEONE under Gestalt system (other than Commoner)
10) DM/GM Always Has Final Word
-Just like normal, if you are crafting an epic masterpiece of a character but it will outshine the others of the group, expect any sane DM to veto it, or else be ready to throttle back what you can do for the sake of having, you know, fun."