This is a collection of tips, but is by no means complete. As new patches are released and new strategies developed, things may change.
Talking to your team is essential to being a great commander.
The biggest thing I can recommend is to get feedback from your team. Ask them what they want and work to make them their best, e.g. If someone says they play a good Lerk, research Spores for them.
Use explore mode to learn what the various structures do.
Holding resource nodes is highly important. Skill being equal, the team with more resources will win. But, you need your team to be able to protect them. Each resource tower costs 10 resources to build, and take 1 minute to recoup their own cost once built. Meaning, if you have a tower being constantly destroyed, it may not be worth it to rebuild until you can better secure the area.
Don't build defensive sentry guns or whips. They are generally regarded as a waste of money. If you insist on using them, place them offensively in forward positions, and not defensively around your main base.
You can leave your command role at any time. If the enemy has managed to slip a single unit into your base while the rest of your team is elsewhere, or if your base is being swarmed while the rest of your team is present, jump out and help fight off the enemy. Simply exit the chair and shoot or bite the enemy to death, then resume command again. The enemy is often caught unaware by a commander joining the fight. All players, including the commander, start with 20 player resources. It is often beneficial to spend your personal resources for the time you may need to help out on things like: Mines, Welders and Weapons for the Marines and Gorge Hydras for the Aliens.
Use your ping functions regularly. Giving your troops a visual cue of where and what to do helps a lot.
If a player is requesting support (asking for Medpacks, Ammo, Nutrient Mist or orders) you can press the Space bar to center your screen on the player.
The marine commander is much more hands on than the alien commander. A marine commander can directly provide health, ammo, and damage absorbing shields(Nanoshield) to his troops. He can also scan for enemies in an area and force recall of forces back to the base. The marine commander also has access to special non-player units.
You often have very little time to respond to a Marine's request for assistance before he dies so it is greatly beneficial to know and learn the Hotkeys to drop Med Packs, Ammo Packs and Nanoshields.
You can assign Hotkeys to a building as well as a group of buildings using CTRL + [Number] where the number is 1 through 9 inclusive. Assigning a building to a Hotkey will place an image of the building above your minimap which will flash red when it is under attack. It is often beneficial to assign your Arms Lab, Observatory and base Power Supply to a Hotkey so you can maintain Marine upgrades and quickly call a Distress Beacon if your base is under attack.
In explore mode as marines, you can recycle all of your structures and start from scratch to learn the tech tree.
You can exit the chair to build things yourself, if no teammates or MAC's are around.
Try to start weapon and armor upgrades as soon as possible from the Arms Lab. Weapon and Armor upgrades take a long time, so try to have your Arms Lab continually researching an upgrade.
Don't drop a second Command Station too early. Everything except Nanoshield and Prototype Lab(Jet Packs and Exosuits), can be built, researched, purchased or used with only a single Command Station.
A solid start as marine commander is to build an Armory, a second Infantry Portal, and an Observatory.
Mines and Welders are solid first upgrades. You can place Mines in your base to prevent early base rushes as well as around Phase Gates.
Put Phase Gates in every base you control, and maybe even a few extras in key locations. This is the absolute fastest way for marines to navigate the map. Having too many Phase Gates can confuse some of the players on your team, so try to limit how many you build.
When sending Exosuits to attack, make sure you have MACs and players with Welders following them to provide additional repair.
The alien commander has less of an active role on the battlefield. Really, the only thing they can activate are abilities on the Shade, Shift, Crag, Cyst and Drifter.
Alien tech is largely based on the number of hives controlled. Each hive, up to three, unlocks two additional buildings. One is a functional support building, the other is necessary for access to two of the six evolution traits. Species specific traits are also researchable based upon how many hives exist (again, up to three).
Crag hives allow the construction of Crag and Shell structures, with the Carapace and Regeneration evolutions.
Shade hives allow the construction of Shade and Veil structures, with the Silent and Camouflage evolutions.
Shift Hives allow for the construction of Shift and Spur structures, with the Celerity and Adrenaline evolutions.
Popular first evolutions are Carapace and Celerity. It is not recommended to create a Shade Hive until later in the game (perhaps as the third hive). Though your requirements may change from game-to-game, it's generally agreed upon that additional health and/or speed will be of more use to your troops in battle than being able to hide will be outside of battle.
All alien structures must be placed on infestation (except for Gorge structures and Hives), and will take damage if the infestation recedes.
Try to get Drifters (they can be created from any Hive) on the field in key places (near your resource nodes, expansion hives and popular Phase Gate locations). Drifters let your entire team see what is going on near them and you can use the Enzyme Cloud ability to increase the attack speed of all Kharaa life forms by 25% in an area. Using Enzyme Cloud can be a great way to take down key marine structures (Power Node, Command Chair, Observatory and Phase Gate) before the Marines are able to respond.
A solid way to start a match as alien commander is to build a few drifters, extend cysts to the nearest few resources, then follow up with a Shell or Spur for evolution.
Always remember to hide and protect your evolution dependent buildings, don't just place them in the middle of your base. If they get taken out, then your whole team loses access to that evolution.
One way you can protect your upgrades is to place the upgrade near a wall and then place Clogs around the upgrade. Another good strategy is to place your evolution dependent buildings at different Hives.