OK, first a few responses, then to the rest of the cards:
Templar: As written, 'you may discard this' implies from your hand; it should specify 'discard this from your Tavern Mat' or 'from your hand or reserve mat' for clarity's sake.
Cloister: Point taken. But there's still an opportunity cost. First you're buying a Duchy's worth of points over Gold or a $5 card; then, once you have the Cloister in hand, you have to either buy a VP Card, or have Cloister continue to clog your deck. If I'm going to spend $6 on a Duchy anyway, fine; but I'm not sure this is as versatile as, say, Farmland, which helps you when you're already greening. But sure, it's an interesting idea, and I look forward to the results of testing it.
Crusade: Mea Culpa; that's what I get for posting at midnight.
Holy See: This does have its niche uses, but is mostly valuable when 1) you only have $6 or $7 late, and feel that the extra point from Duchy won't swing the game; 2) Your deck is Treasure-Based, rather than Engine-based (because Engines wouldn't want Treasures clogging up their next hand. So again, a niche card--not necessarily a bad one, but still one with limited overall value except perhaps in a Holy Order-only Kingdom.
Iconoclast: I'll trust the forum's judgment, then.
Penance: I think I probably misread this card. But in any case, would it be better as something along the lines of 'Gain a Copper; if you do, + [3?] Cards'? This would make it a niche card like Beggar that has some useful combos. It would retain the self-penalizing aspect, and you could keep the on-trash bonus if you want.
On to the other cards:
Reliquary: Seems weak; maybe a little better than Trade Route, but it scales well with multiplayer and may be a decent counter to the likes of Cultist.
Black Mass: Superficially similar to Quest. Only problem is that it's completely useless in games without Cursing attacks. Maybe you could have it discard a Curse or Victory card costing $3 or more (so that it doesn't trash Estates or Overgrown Estate)? But I like the concept.
Indulgence: I think this would be weak even if its ability weren't a one-shot. Sure, in some games you'll want one of these for the cantrip +Buy, but it's only better than Market Square in games that have both Cursing and no Trashing. Maybe you could instead have it read, 'You may trash this and another card from your hand; if you do, +2 VP' for a similar but more versatile effect.
Iconographer I like it, but the text could be improved to
+1 VP
Choose one: Trash two Treasures from your hand; or trash this and gain a silver
Holy Vestment If I have 3 Holy Vestments on my Tavern mat and decide to call all of them at the start of my turn, do I draw 6 or 9 cards? (If I have to resolve them sequentially, I get 3 from the 1st HV, 2 from the 2nd, 1 from the 3rd; if they resolve simultaneously, then they each draw 3 cards). I don't know of a good reading to distinguish the two possibilities.
Funeral: As a rule, Dominion cards either give +Coin or +Cards but not both at the same time. I think this card would be better off giving +Coin only; there are precedents for one-shot coin producers (Spoils, Death Cart, Pillage), but not one-shots that give +Cards, except for Madman, which is intentionally overpowered. (I suspect that this means that one-shot that gives +Cards has already been tested and found wanting). Also, you might want to have it cost $3, because Dark Ages introduced a division between 'good trash' that costs $3 or more, and 'Bad Trash' that costs $2 or less.
Pardon and
Missal I agree with Library Adventurer
Collection Plate Wouldn't it be better to just deal out Coppers, because 1) a single Charity is not all that bad, as LA said, and 2) Charity seems to weak to use up a card slot, even if it's not in the Supply.
Confession Donald X has already said that he's tried a discarding Lab for $4 and it didn't work (see the Secret History of Adventures, or the Fugitive page on the wiki)
Excommunication--thematically, it would be great if this could only be trashed by a Chapel, Bishop, or other church-type card, but I realize that's not possible to work; otherwise, would it be better to make this 'When you trash this, gain two Coppers'? That way, you could still trash it, but it would be painful.
Overall, you have a good set of ideas, though, with some interesting cards already and some more that have promise.