Below is a non-comprehensive list of surnames which are pronounced non-intuitively. (Or one could argue that they are pronounced perfectly sensibly but the spelling is non-intuitive.)

I've also included a count of how many times each surname applies in the 2006/07 Brighton telephone directory, to give you an idea of the relative importance of learning to pronounce each name correctly.

Spelling Pronunciation Freq
Althorp Owltrop 0
Ayscough Askew 0
Beauchamp Beacham 12
Beaudesert Belzer 0
Beaulieu Bewley 0
Belvoir Beaver 0
Chandos Shandos 0
Chisholm Chiz'm 11
Cholmondley Chumley 0
Cockburn Coburn 10
Colquhoun/Colquhon Co'hoon 6
Cowper Cooper 3
Crawshaw Crayshaw 2
Dalziel Dee'el 6
Farquhar/Farquar Far'har 2
Featherstonehaugh Fanshaw 0
Fiennes Fines 0
Gower Gore [1] 40
Greenhaugh Greenallsh 0
Home Hume [1] 3
McKenzie/MacKenzie Macinnie [1] 59
Magdalene Maudlin 0
Mainwaring Mannering 1
Marjoribanks Marshbanks 0
Menzies Mingis [1] 5
Ruthven Ruffen 0
St John Sin-jen 5
Trywhitt Territ 0
Urquhart Urhart 5
Wauchope Warkup 3
Wodehouse Woodhouse 1
Woolfhardisworthy Woolsey 0
Worcester Wu'ster 2
Wriothesley Roxley 0
Wymondham Wind'am 0

***

1 Also pronounced as spelt.