Your bitcoins aren't lost, the bitcoin network knows they were sent to your address, and your current balance. However, you need your wallet in order to
spend them, so if you loose the wallet file, effectively your coins are gone to you. Have a look
here for help in finding the correct wallet file that you had previously been using. Make a secure backup of it (on USB keys, encrypted passworded 7-zip on a secure storage site, etc) so it will never get lost even if someone breaks in to your house and steals everything computer they can see.
You should not use the same wallet on two installations at the same time, the wallet contains a list of one-time-use private keys used for signing your payments when you send, and one bitcoin may generate private keys in a wallet the other wallet doesn't know about.
After you have discovered the wallet file, decide on the one place you will use it and put it in that bitcoin's user directory. If it seems that you are still missing payments or balance and you know the wallet is the correct one with the addresses payments were sent to, go to a console window (or on windows, open a cmd window and go to the C:\program files\bitcoin directory), and run
bitcoin -rescan, which will look through all the transaction blocks to discover any transactions for your addresses that were missed.
