One of the common poor design decisions I have seen in the field is using a single Web Application to host everything (SSP Admin, My Site & any other team sites); to me this is like putting all your eggs in one basket; instead consider creating multiple web applications one for each of the high level functional segments of your farm; so one to host SSP Admin another to host My Site and maybe one or more to host your actual team sites and organization content. also consider creating multiple content databases per web application to host the various site collections you might provision in the context of each web application so that you drive a bit more fault isolation and resilience into your design.
So here is what happens; when you create a web application in MOSS 2007 you also create an associated content database (Example: WSS_Content) then you will need to create at least one site collection in order to be able to start browsing the web application you had created. so far so good.
Now over time your customer, team mates, etc.. will ask you to create more as some might ask for a site with a calendar and a document library and others might ask for a performance and business intelligence site; over time each new site collection you create gets stored in that original content database so in a way you end up with a possible single point of failure content database; instead why not create additional content databases and split each of these site collections across multiple databases? doing so establishes a bit more fault isolation into your design and gives you the flexibility of more granular backup and restore abilities.
More to come on this topic..