Well I had the same problem....Then I bottled......Carbonated well, but just found out today that if you leave the beer on the yeast too long its not good. I had one 3gallon batch and one 5 gallon batch in a secondary for 3 months....The beer is drinkable but has a ...ummm plastic type taste. I took them to the homebrew shop today to find out what the taste was. They said I left the beer on the yeast too long....And there is some term that describes what the yeast do to themselfs. Anyway the beer sucks pretty much. The only thing is I had no temp control which added to the problem. I guess if you got a lager going its cool but ales on the yeast too long is not a good thing.
After sitting on the yeast that long you are likely to encounter some off flavors as Dark Ale had mentioned. This is caused by Autolysis, which is when the yeast actually starts to consume itself due to the lack of anything else to consume. Best advice I can give is to bottle it like normal and then taste it. Worst case is you have to pour it out, but best case is, after a little aging, it tastes ok. Won't hurt to try.