Hi gopikshnan,
There is not problem technically in these concern. You can always use the App_Code Folder for these purpose and you can go for Seprate project(Class Library) as well.
There is no problem in either of the case, but the best approach I would suggest is the Seperate project. Because using separate project you can handle large volume of files easily.
Secondly Let say your Busness logic is subject to Share between different projects.., you can use just the .ddl of the data access layers class library.
The App_Code shoud contain general utilities class which methods like Calculate Tax let say which you are using almost of the page.
Thats it..,
Thanks and Regards,
Rk_Hirpara