Cut and paste into a spreadsheet, then take maybe 10 minutes to identify my top 50-65 or so, depending on the qualiity of the board. Then I'll spend maybe a half hour to rank the top position players from 1 to whatever in my spreadsheet, another half hour to rank the top pitchers from 1 to whatever in my spreadsheet, then another 20 minutes or so to merge the ranked hitters and pitchers together into a single 1 to whatever list, again only within my spreadsheet.
Quite often I'll do this final merge of the two lists (position and pitchers) on a different day from when the first two lists were ranked. Gives me a bit of a fresh perspective and I'll sometimes find myself tweaking the original rankings.
I'll also pay special attention to the top "x" number of players in my merged list, depending on where my first round pick is. I want to try to guarantee that I've got the first round pick solid.
Then I'll go through the rest of the position players for around 10 minutes to identify some depth to fill out my minor league rosters. Add these guys at the end of the first list, then do a single session of doing the manual rankings in the game itself.
If I get all of this done with a couple of days to spare before the draft, I may do some final tweaking, but usually I feel that after I've done all of the above I have my rankings in as good a shape as possible. Overanalyzing will make me nuts.