In season 5, Amy developed a "girl crush" on Penny. Some of her comments were very innocent at first, and really non-sexual, more complimenting Penny's golden hair or flawless skin in a way that suggested Amy kinda worshipped her and was really in awe of being friends with the beautiful, popular girl. The comments got a lot of laughs, though, and then the writers ran with it and made them creepier and more sexually inappropriate. Then the audience stopped laughing at them, and they started to get written out and pretty much suddenly vanished altogether. At Comic Con after the 5th season, the writers were asked about the "gay for Penny" stuff coming out of Amy's mouth, and Steve Molaro looked particularly guilty and said it was a joke which got taken too far and that it got axed fairly quickly when audiences stopped laughing at it.
Amy was always meant to be portrayed as having a girl crush on Penny, but moreover, it was supposed to be an extension of the fact that Amy never had any friends in her life (It would seem she was extremely isolated by a very over-protective mother) so when she became "besties" with the very definition of the beautiful, blonde, popular girl, Amy finally felt she fit in somewhere and in some ways let the joy of having real friends for the first time in her life go to her head. It was never meant to suggest that Amy was a lesbian, or bisexual. It's been clear Amy was meant for Sheldon from the get-go, and is heterosexual. (In fact the first time she seemed to have gotten turned on is by Zack.) The writers just got a little loosey-goosey with a joke and then had to reign themselves in later.