PCS has an "all time" ranking: I have no idea how comprehensive their list of historic results is, but they have Valverde just moved in to the second best of all time.:
1 1 - Merckx Eddy 2599
2 3 ▲1 Valverde Alejandro Movistar Team 1348
3 2 ▼1 Hinault Bernard 1271
4 4 - Cipollini Mario 1150
5 5 - De Vlaeminck Roger 1133
6 6 - Boonen Tom 1083
7 7 - Kelly Sean 1007
8 8 - Cavendish Mark Dimension Data 1002
9 9 - Moser Francesco 989
10 10 - Van Looy Rik 977
11 11 - Zabel Erik 973
12 13 ▲1 Contador Alberto Trek - Segafredo 962
13 12 ▼1 Cancellara Fabian 953
14 14 - Coppi Fausto 946
15 15 - Anquetil Jacques 943
16 19 ▲3 Gilbert Philippe Quick-Step Floors 939
17 16 ▼1 Binda Alfredo 936
18 17 ▼1 Sagan Peter Bora - Hansgrohe 932
19 18 ▼1 Bartali Gino 902
20 20 - Greipel André Lotto Soudal 882
21 21 - Petacchi Alessandro 881
22 22 - Maertens Freddy 869
23 23 - Gimondi Felice 861
24 24 - Jalabert Laurent 857
25 25 - Saronni Giuseppe 844
26 26 - Indurain Miguel 783
27 27 - Freire Oscar 732
28 28 - Museeuw Johan 730
29 29 - Rominger Tony 722
30 30 - Rebellin Davide Kuwait - Cartucho.es 718
Changes are during April
http://www.procyclingstats.com/rankings.php?code=all-time-ranking