Sure you can condition in a carboy. The only bits you have to worry about are
1) Very extended times (many months) and you may run in to slow to carbonate/failure to carbonate issues if you loose enough yeast (yeast half life at cellar temps is around 2 months IIRC). This has never been an issue for me, though I think the longest I've cellared a beer was a RIS that sat in the carboy around 3 1/2 months before I bottled it. It carbed up in less than 3 weeks.
2) Very extended times can also raise the risk of oxygenation or other problems. Again, not overly likely to occur, but it is at least possible.
3) You'll probably still need some bottle/keg conditioning time no matter how long you condition it in the carboy. Especially bottling you have to wait for the yeast to eat up the bottling sugar, carb the beer and settle down. It isn't much sugar that the yeast is eating, but every single beer I've ever brewed has taken at LEAST 3-4 weeks after brewing to hit its peak (often times more like 5-8 weeks, though some heavier beers have taken months before I thought they had hit a peak. Though peaking doesn't mean it gets bad suddenly, might take months before I notice it isn't as good as it once was). Where I "aged" a nut brown for 8 weeks in the carboy before bottling of bottled a porter after 3 weeks. Always seems to take 1-2 weeks after the beer is properly carbed before it settles down and is its best.
Of course with some brews that require extended aging to hit their peak, it was only around 4 weeks or so before it was well conditioned, because I left it in the carboy for a couple of months first, instead of probably needing to have bottle conditioned for 2-3 months first (or longer).
