The top logo is awful (both design and 'noise')!
and the 'ex timer' image is pretty nasty, try higher quality jpg.
Also, the home page is centred fixed width, but some pages are left-aligned fixed, some are 100% across the page (you need to be consistent)
Use fonts other than Times/default, especially for source code (using monospace fonts look good and is what people are used to)
Login part of chat looks like it was made in 5 minutes and does not do the nice chat justice (it will scare people off). Make it look nice so people actually discover the chat! Maybe also indicate how many people are in the chat room on the home page? Nobody wants to click, invent a name, then log in, just to find out they are talking to themselves. You may want to change index.html to .php to make this easier.
Several links on the left of pages do not follow the style (quick look at source reveals the problem and reveals that a style sheet would be a much easier way to apply the hover effects! You need to copy the effects 'class'..'href' from the working links and put them after '<a')
Having been very critical, there are several good points about the design - the menu is nice; sparse use of colour is effective, and where used, it looks good and goes.