I like Konerko over Lopez. I agree that Bonds should not be considered in a keeper league due to his knee issues.
Konerko has hit 41 and 40 homers the last two seasons with an average around the .280 mark. His On Base Percentages (OBP) are .359 and .375 for the past two years. His age is 30 so he is on the downside of his prime years.
Looking at his career numbers, with the exception of his lousy 2003, Konerko has been a pretty consistent hitter as is evidence by his plus .349 OBP as a regular in the Chicago line-up. The last two years have seen him improve in his power numbers of his career as is evidence by his posting his top two career Slugging Percentages of .535 and .534. I believe Konerko's numbers may drop a bit this year from the last two years, but overall I think he will be a better offensive tool than Lopez.
Lopez had a good year last year hitting .291 avg/.352 obp/.486 slg with 23 homers at the shortstop position. As a life long Reds fan, I really hope Lopez can improve on those numbers. But, looking back on his career numbers, last year was the first time he had hit over 10 homers in a season. To be fair, it was also the first time he had over 550 At Bats (AB). Last year, Lopez hit a homer every 25.2 AB compared to his previous career number of a homer every 41.8. Lopez is 26 years of age and you would expect his power to develop as he ages; but with the spike up in homers last year, you can paint me as being skeptical that he will hit 23 plus homers this year. I hope I'm wrong though.
One metric that I use in fantasy baseball is Isolalted Power (ISO). It takes into account doubles, triples and homers. It is similar to Slugging Percentage; but instead ot counting singles as part of total bases, it isolates the power results and puts them into format similar to a hitters average. The formula I use is a modified version from Baseball Prospectus: 2B+3B+(HRx3)/AB. You can read about Isolated Power in this article from athomeplate.com from Ray Flowers:
2001 .136 ISO
2002 .149 ISO
2003 .076 ISO
2004 .155 ISO
2001 thru 2004 .132 ISO
2005 .186 ISO
2004 .258 ISO
2005 .250 ISO
1997 thru 2005 .208 ISO
I'd keep Konerko over Lopez and then with your first pick take the best power remaining on the board regardless of position. There is something to be said for positional scarcity; but with only three keepers, you are essentially beginning the fourth round of a traditional style do-over draft. You shouldn't pass up on any power hitter in the first three rounds of a draft and if a power hitter is still on the board at the fourth round, you should go and get him. I wouldn't let Konerko be on that draft board if it was me. Early mid rounds is when I would start to think about positional scarcity.
I hope this helps.