It looks like he was very good in each of the past two years. I am not going to discuss the issue of what percent of his flyballs became HRs. That is important, though. Derek Carty has written about the idea that pitchers might differ in their ability to prevent flyballs, but not in their percentage flyballs that become HRs. That article is at Using FIP to evaluate pitchers? I wouldn’t.
I am going to look at Lincecum's HRs allowed relative to the league average. The data I used comes from the Lee Sinins Complete Baseball Encyclopedia. Here is how it works. Suppose a pitcher gives up 10 HRs while the average pitcher would have given up 20. You divide 10 by 20 to .5. Then 1/.5 = 2. That gets multiplied by 100 to give you a rate of 200.
In 2008, Lincecum gave up 11 HRs while the average would have been 26 (actually it would be about 25.85 but when you call up this kind of data with the Sinins tool, it does not have decimals, it just rounds everything.) So his rate for 2008 was 235. In 2009 he gave up 10 while the average would have been 25. His rate was 249. This seems pretty good, two straight years over 200.
Now being a right-handed pitcher, he gets an advantage pitching in AT & T park where it is tough for lefties to hit HRs. Bill James has a HR factor their for left-handed batters over the years 2007-9 of 88, meaning that it allows a rate to lefties equal to 88% of the league average. The righty park factor is 93.
So I adjusted his HR totals based on these park factors. In each year, I raised his HR total vs. righties by 3.5% since AT & T allows 7% fewer HRs to those batters and the Giants play half their games there (using Baseball Reference, he actually faced about 51% of his batters at AT & T (didn't mean to go Empire Strikes Back on anyone)). So I will just stick with one half. His HRs against lefites get increased by 6%.
He gave up 7 HRs to RHB in 2008. Raising that by 3.5% makes 7.245. He gave up 4 to LHB and raising that by 6% leaves 4.24. so his adjusted HR total for 2008 is 11.485. In 2009, he gave up 2 & 8 HRs, respectively, to RHB & LHB. Adjusting that would leave a total of 10.55. But if I recalculated his HR rates for the two seasons, they are 225 & 236, respectively. Still very good (by the way, he gave up no HRs at home in 2009).
How many pitchers have had back-to-back seasons with a HR rate of 200 or higher with 200+ IP in each year? I only looked since 1920, but it is only 17. Some of those pitchers did for more than 2 straight years. Greg Maddux did it 5 straight. To see all the cases click here. Eppa Rixey did it in 1923-4 and 1927-9, too, but he did it in a very tough park to hit HRs. The Reds park, from 1920-29, it allowed only 22% as many HRs as the average park in the NL! (that is according to the STATS, INC. All-Time BASEBALL SOURCEBOOK). The total number of consecutive occurrences is just 25, including Lincecum these past two seasons.
I also found the top 100 combined two year HR rates using only pitchers who had 200+ IP in both years. Since 1920, I found 2,310 cases of a pitcher having 200+ IPs in back-to-back seasons. To see the top 100, click here. When you see a year in that table, it is the 2nd year in the case. The AVG is weighted by the IP in each season. Sad Sam Jones was a righty pitching in Fenway when it took a long poke to get a HR by a LHB (I think it was before they had the bullpens out in RF). He gave up just 1 HR in one of those years. Notice that Reds pitchers from the 1920s-30s are up there again (Rixey, Luque and Donohue). Maddux 1994-5 is 9th with 406.1, basically being 4 times better than the league average. It looks like the only guys ahead of him are guys who got alot of help from their parks (I don't know about Coveleski). I don't think Maddux got much help from his. James has Atlanta with a HR factor of over 100 from 1993-6. Lincecum from 2008-09 is 54th. Even with the adjustment I did above, I think he would fall to about 63rd. Out of over 2300. Not bad.