I read somewhere that WU's getting lost is a known issue - one of the suggestions to correct this was to reinstall the app.
To reinstall it there should first be an easy way to kill it.
I can't find a single exit button anywhere, so I had to manually get into task manager to kill UD.exe... after first killing rosetta-something that apparently just loaded a new WU when killed - this should be streamlined some more, so that one could exit/reinstall in one easy operation.

Secondly.
My 2ghz p4 without HT seems to be working those proteins faster than my 3ghz p4 with HT... so there doesn't seem to be support for HT in the app as far as I can see. (Rosetta only uses 50% of cpu on my 3ghz, and can use up to 99% on my 2ghz... a serious amount of cpu power bleed there.)

Third.
When changing profiles for devices on the wcg pages this doesn't update in the clients, making one stuck with the poor rating of 20 for storage of 1GB which is default until a new WU is loaded. The profiles should be selectable in the client itsself so it'd know straight away what settings it's supposed to use.

Fourth, fifth and so forth... (Just other random suggestions)
Someone has recently started fiddling with taking advantage of the number crunching abilities of GPU's... as they are said to be far superior to that of the CPU. Would it perhaps be an idea to incorporate something like this into WCG? As this would worst case scenario more than double the amount of processing power out there?
And, by the way... if the gpu processing power was made available to wcg - this might be one more incentive to get people to join the network - as wcg could also provide this extra power for the user when the computer is in use. A win win situation, without money involved... that's not often.
I guess it wouldn't be completely free, as the guys developing that technology probably wouldn't want to give it away for free... but who knows. It's a worthy cause :)

Stats and details within the client would also be a nice touch.
Realtime comparisons with the other people on the team and so on.

Think I'm out of ideas for now... :)

http://www.worldcommunitygrid.org/forums/wcg/viewthread?thread=296 <- found a solution for the HT problem here, but this sort of thing would do good to be built in to the ud/wcg client.