Weather and Clock
For the Weather, AccuWeather is fine for me. It has hourly and 15 day forecast, lots of locations supported, reasonably accurate.
If you need a World Clock (e.g. different time zones), an iPad only app called The World Clock is my choice. It supports very large number of locations (way larger than the Apple's Clock), has a beautiful world day/night map and some nice features, but lacks alarm clock and timer options. It is worth $1 IMO.
If you need an accurate time, there is an app called Emerald Time (universal - iPhone and iPod), it gives accurate time using NTP.
If you need alarm clock, be aware that none of the apps on the app store will fire an alarm if you exit the app. This was mentioned already, but I would highly recommend NOT to jailbreak the iPad to get the functionality. The iOS 4.x update for the iPad was promised by Apple "This Autumn". Better wait few months.
Who knows, may be Apple will port their Clock app as well?