Guardian website - all free - The prize crosswords available are AZED, EVERYMAN, SAT PRIZE & MONTHLY GENIUS.
Times Crossword club - £24 to join for a year - then all Times crosswords are available
Telegraph - similar to Times, not sure of the price
Independent - don't think they are on line at all
Don't know of any others. Hope this helps.
(I joined the Times Crossword Club a few months ago. It's good because you can enter many of the crosswords online & thus save postage!)