I figured out the solution to the remote app connection problems.
Remote app is a free application which turns iPhone and iPod Touch (firmware 2.0) into a remote control for iTunes and Apple TV.
Remote app requires bonjour service to be running on your PC/Mac to interact with iTunes.
Bonjour service listens on the port no. 5354, so just forward the port no. 5354 on your router for both udp and tcp connections, so that iphone can connect to bonjour service on your computer.
After port forwarding restart your router and,
1. start the remote app on your iPhone/iPod and click “Add Library”
2. start itunes and you will see your iphone/touch under devices list
3. enter the code and have fun with your wireless remote controller.
I read the bonjour document which says that we must forward our port 5353, but as I noticed on my computer bonjour service is listening on port 5354!
So there is something with bonjour, but Apple doesn’t care whatever their customers have to face be it non-working DNS Patch or iPhone remote.