Black Templars have three different commanders to choose from, plus the option to take a command squad.

Emperor's Champion

The emperor's champion is a compulsory choice for Black Templars, and not a bad one at that, but he is highly overrated in my opinion. For 105 points you get am improved veteran sergeant, that is only mediocre when compared to the stats of other HQ choices. What makes him worth his points are his special rules: His power weapon grants him a strength bonus and can alternatively be used as a power fist, plus he can challenge other characters. A lot of gamers fear his ability to call challenges, but his stats will make it a risky choice against anyone but unit champions. His armour and invulnerable save can carry him pretty far, but that's no guarantee. Other HQ characters will usually turn him into red paste swiftly. Once your opponents have learned this, your emperor's champion will be easy prey.

The emperor's champion is best used in combination with another unit. In smaller games I recommend a Black Templar's squad with close combat weapons and a power weapon: The unit will take care of the masses, while the emperor's champion can take out big nasties. In larger games an interesting option is to add him to a unit of terminators: The terminators will wreak heavok, while the emperor's champion takes on any power weapon or power fist that comes their way (that's as long as it's carried by a character).

On a side note: It is always a matter of debate how the emperor's champion is counted in regard to army composition. It is stated clearly that he does not use up any choices from the force organisation chart. The first consequence is undisputed: You can take two HQ choices in addition to the emperor's champion, effectively giving you three HQs. In return I take it that the emperor's champion does not fill up the one compulsory HQ choice, meaning you must always take a second HQ.

Marshal and High Marshal

Black Templars only have two choices of Space Marine commanders, equal to a commander and a force commander. The exclusion of a simple leader means you need to spend more points on your HQ. Therefore I would always equip a marshal or high marshal with at least a bolt pistol and power weapon and send him into close combat. Otherwise their improved stats, which you payed for in points, are wasted. The largest draw back to these HQ choices is their inability to take an invulnerable save, as the iron halo is already taken by the emperor's champion. For fluff reasons I would take a marshal or high marshal as third HQ in larger games, but otherwise I prefer a chaplain any day.

In addition to their improved stats all Black Templars' characters are equipped with purity seals. It is yet to be seen how they will work in 4th ed.

Chaplain

Chaplains are very fitting characters for an army like Black Templars, that have strong faith and seek to decide battles in close combat. That a chaplain has good stats and is already equipped with a power weapon (crozius arcanum) and an invulnerable save (rosarius) makes taking him a no brainer. He is probably the most effective character for his point costs in the game. He is my second HQ choice next to the emperor's champion in every game with Black Templars.

Chaplains should be attached to another unit, like all characters. As you already have the emperor's champion, I would use the chaplain's ability to take a bike or jump packs as equippement to enforce one of your fast attack choices. This will probably become even more important in 4th ed.

Command Squad

Command squads are not an HQ choice of themselves, but have to be taken in addition to an HQ character. This is the only unit in a Black Templar army that can have a veteran sergeant. If you take a command squad, you can either give them ranged weapons or gear them up for close combat. In my opinion they are too expensive to give them ranged weapons, but it can be an option to make them more flexible and add some extra long range punch to your army. If you do so, don't forget to take a techmarine with signum to re-roll failed hits.

Gearing a command squad up for close combat can give you a huge number of power weapons and/or power fists: Veteran sergeant, apothecary, techmarine and standard bearer can all get weapons from the arsenal, but this will make the unit very expensive points wise. Adding a transport is almost compulsory for such a unit. A land raider would be fitting, but again very expensive. A high marshal's command squad can easily cost over 900 points, making it not a very realistic option. On the other hand a simpler version in a rhino costs less than 500 points, making it an interesting choice in 2000+ points games.