A Google Groups thread has discussion about the questions one webmaster has in regards to his country-coded top-level domain (ccTLD), moonri.se.
There are a couple interesting points we can learn from this thread.
(1) As the Google help document states, you can only set the geographic target of your site in Google Webmaster Tools, if your using a generic TLD, such as such as .com or .org or .net and so on. If you are using a ccTLD, such as .se, .co.il, and so on - you can not set your geographic target in Webmaster Tools.
(2) More importantly, Googler, JohnMu said that having a ccTLD as a domain should not hurt your rankings in the main Google.com search results. John explains that by having a .se ccTLD, you might expect that a Swedish searcher "would see it [your site] somewhat higher" in the search results when searching in Sweden. But on the other hand, John said that this "doesn't mean that it's lower in the US than it would have been if it were using any other top level domain."
According to the help document on setting your geographic target information, you should know that that may have an impact on your Google.com rankings. The document says:
If you're targeting users in different locations - for example, if you have a site in French that you want users in France, Canada, and Mali to read - we don't recommend that you use this tool to set France as a geographic target.
This does not mean a ccTLD would rank worse in Google. That is kind of obvious, because ccTLDs do not qualify to use the geographic target feature. But a generic domain which uses that feature may be impacted by changing that criteria. If that is the case, it just seems logical to me that the same would be applied to a ccTLD and your rankings would suffer a bit in the main Google results. Of course, the Google document specifically mentions if you want to rank well in Google France, then don't set your geographic target to Sweden.
There you go, some food for thought.
Forum discussion at Google Groups.