Here's my list:
A cocoa, diamond, diaper, elementary, artistically, equivalent, aesthetic, carafe
B debt, subtle, subpoena, lamb, comb, thumb, plumber, etc.
C muscle, antarctic, acquire, blackguard, czar, victuals, Antarctica
D handkerchief, sandwich, Wednesday, handsome, and (pronounced without the 'd' in casual speech)
E vineyard, vegetable, stopped
F fifths, halfpenny (obviously obsolete, but hey)
G assignment, campaign, gnostic, cologne, gnarl, gnome, gnat, sign, reign, foreign, phlegm, impugn
H honest, hour, honor, rhythm, rhinoceros, ghost, what, why, when, herb (U.S. pronunciation), thyme, Thailand, Thames, him, her (as in "get him", "get her", etc.), chihuahua, John
I family, business, parliament, Salisbury [steak], lieu, lieutenant
J marijuana, Juan*
K know, knee, knob, knife, knight, knot
L half, calf, talk, walk, should, could, salmon, yolk, chalk, folk
M mnemonic
N damn, column, autumn, hymn
O chocolate, people, leopard, jeopardy, subpoena, phoenix
P pneumonia, psychology, pterodactyl, receipt, cupboard, coup, corps
Q lacquer
R surprise, February, chitterlings
S island, debris, apropos, bourgeois, rendezvous
T soften, Christmas, castle, fasten, listen, mustn't, ballet, gourmet, tsunami
U building, circuit, guard, rogue, physique, tongue
V fivepence ("fippence"), have (in "could have" [coulda], "would have" [woulda], etc.),
W answer, sword, two, write, wrist, wrestle, wry, who, whole, Greenwich
X faux pas, [grand] prix
Y prayer, says
Z rendezvous, laissez-faire, oyez

* Yes, Juan should be [hwan] (or better yet, [xwan]), but just like many English speakers pronounce 'wh' as [w] instead of [hw], we pronounce Juan as [wan].

Digraphs:
CH yacht, chthonic
GH night, light, etc.
PH phthalate
TH asthma, clothes, sixths

I agree that double letters (like the 'ff' in 'cliff' or the 'zz' in 'jazz') don't really count—they're both part of the same pronunciation.

As far as foreign words, if any monolingual native English speaker would use it as an English word, it definitely counts. So, for example, my semi-literate monolingual English speaking neighbor might talks about a "midnight rendezvous" without even knowing how it's spelled, and no one gives a second thought to the term 'grand prix' when they're at the racetrack, even if they do recognise it as French. Also, words like 'tsunami' are clearly foreign, but the fact that it has a separate pronunciation in English (without the 't') makes it count.

For the sake of interest, I'm going to exclude place names altogether unless they're common international place names like Antarctica.

For those saying that words like 'talk' and 'walk' don't count because they change the pronunciation, maybe a better way to think of it is like this: If someone (a child learning to read or a non-native speaker, for example) pronounces the letter and it sounds wrong, it counts as a silent letter.

And yes, obviously it all depends on your dialect. The best responses are words with letters that are never pronounced by native speakers in casual conversation.