Capstone feats are generally meant to be a bit over budget. In many cases, they grant what would be class features that would be iconic (showcasing the class in a unique way). E6's nature very much rewards multiclassing for most martial roles, and capstone feats serve as a way to ensure single classing is viable, so their power is intended to be real. However, the choices are still pretty much untested, and unlike standard D&D, Zem and I have as much experience with E6 as everyone else here- to say, none excepting the current game. Some of the capstones are from the standard E6 capstone set- I won't distinguish among those and ours further, but to link to the E6 list here:
http://dungeons.wikia.com/wiki/E6_(3.5e_Sourcebook)/Rules
Note that because E6 is not closed content, we have the feats on the public forum, and would show up in google searches for someone else trying to homebrew and wanting to see what others are doing.
Barbarian:
Unbreakable into Greater Rage is the big money here- a two feat cost for definite payback. Greater Rage is the more desirable one, which is why it is gated behind the defensive / utility option- to avoid punishing the player for wanting to play a barbarian with an awesome rage, but bribing him to save a feat by just buying the offensive one. The others are a 3.X-ified version of Pathfinder's "rage powers". Rage Powers are a baseline class feature in Pathfinder, and give you perks when raging. The perks are normally worth about half a feat or so. This bundles some up for use in 3.X.
Bard:
We halfassed Bard. Partly this is because there's a lot of really good bard feats in our bigger list, but the main reason is we knew no one was aiming at bard as a PC for this game, and Zem didn't have a huge need for combat bard NPCs. I still think we should make this better- any improvement suggested?
Cleric:
Power over Death is good if you're in an undead campaign, which we certainly appear to be. Extra domain power into Extra domain access is the intended combo, and IMO it is not that great. Extra Domain Power kind of is, but Extra Domain Access is only great if your god has a third domain where the spell access is incredible. I don't think these capstones are that strong, but I'll also say that single classed cleric is a strong choice, and other feats available already put him in a good spot. Still, if anyone has ideas, post'em.
Monk:
The one to make your punches better is good. The others are also good. "You can the use of Improved Evasion", indeed! Monk has plenty of easy iconic things to pick from, so we did.
Fighter:
I feel these are strong. I feel Martial Veteran into anything is pretty strong, and Experienced Veteran and Armor Mastery are both effective and powerful in E6. I really feel we did a good job on Fighter.
Paladin:
These are customized for Zem's world, making them totally awesome. The mechanics could be used normally, of course.
Inner Purity into Justice Undimmable is a pretty good use of two feats, but into both Justice Undimmable and Hand of Agnelo should be a very good use of three feats. If this isn't the case, I'll be kind of surprised- minor swift action healing plus smites being usable twice each gives the Paladin some of the powers of the much more powerful Pathfinder version. The two campaign specific ones are less obvious as to whether they'll be powerful or not.
Ranger:
Putting Boon Companion as a capstone prevents cheeseball multiclassing with the ranger. Natural Attunement offers an extra spell slot (moar entangle!) while also putting the niche woodland stride on the table, and Wilderness Agility gives the ranger evasion while also adding the swift tracking class power. Each of these offers an iconic class ability in a bundle.
Druid:
We probably need a caster variation here, but druids are in great shape in E6, and this one is the standard capstone. We did nothing, but druid doesn't feel bad multiclassing and won't feel bad taking this capstone.
Rogue:
The money here is the extra sneak attack damage. The standard capstone of rogue talents takes a backseat to extra damage.
Sorc, Wiz:
We are lazy. Also, these classes are already single classed. Personally, I'd still like to add them, and I view getting a sorc capstone in there is pretty important given that we actually have a 6th level sorc on team. I don't feel either of these classes ever wonders how to spend a feat in E6, however, with Extra Slot and Extra Spell available. I just posted some notes on those two in the private forums, because the hybrid version we ended up with is confusing and has typos.