iphoto 9.6.1

The update is available:

Go to the App Store and check out the Purchases List. If iPhoto is there then it will be v9.6.1

If it is there, then drag your existing iPhoto app (not the library, just the app) to the trash

Install the App from the App Store.

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Sometimes iPhoto is not visible on the Purchases List. it may be hidden. See this article for details on how to unhide it.

http://support.apple.com/kb/HT4928

One question often asked: Will I lose my Photos if I reinstall?

iPhoto the application and the iPhoto Library are two different parts of the iPhoto programme. So, reinstalling the app should not affect the Library. BUT you should always have a back up before doing this kind of work. Always.

Or, just delete iPhoto and you won't get the update message

I've downloaded El Capitan and I know that iPhoto was replaced by Photo.

Would you prefer to continue to use iPhoto or migrate your iPhoto Libraries to Photos?

If you update to iPhoto 9.6.1, you can continue to use iPhoto on EL Capitan.

For the past few days iPhoto had been gone completely from the App Store, but day before yesterday Apple returned older purchases to the App Store. There may still be maintenance work going on, so try again later, if the problem persists.

http://www.macrumors.com/2015/09/29/older-software-returns-mac-app-store/

Which iPhoto version do you currently have installed? Has that version been purchased from the App Store or did it come preinstalled?

If your iPhoto version is associated with your AppleID at the App Store, Barney's user tip should work, once the App Store is back to normal:

See: Can't Update iPhoto because it is not available in the App Store

But if you simply do not want to be bothered with the iPhoto 9.6.1 update notification any longer, delete the incompatible iPhoto version from your Applications folder (the application, not your iPhoto Library) and restart the App Store or hide iPhoto from your purchases (Mac App Store: Hiding and unhiding purchases). But keep a backup copy of the iPhoto application, just in case.