I have a few custom logfunctions that are extensions of cat. A basic example is something like this:
catt<-function(..., file = \"\", sep = \         
        
I thought I'd add the progress made so far, based completely on Andrie's work. Pretty sure other people will enjoy this, so it is now a part of a package I'm developing (not on CRAN but on R-Forge for now) called addendum (including documentation) after the nightly build.
Function to find the 'current lowest named function' on the callstack with some bells and whistles:
curfnfinder<-function(skipframes=0, skipnames="(FUN)|(.+apply)|(replicate)",
    retIfNone="Not in function", retStack=FALSE, extraPrefPerLevel="\t")
{
    prefix<-sapply(3 + skipframes+1:sys.nframe(), function(i){
            currv<-sys.call(sys.parent(n=i))[[1]]
            return(currv)
        })
    prefix[grep(skipnames, prefix)] <- NULL
    prefix<-gsub("function \\(.*", "do.call", prefix)
    if(length(prefix)==0)
    {
        return(retIfNone)
    }
    else if(retStack)
    {
        return(paste(rev(prefix), collapse = "|"))
    }
    else
    {
        retval<-as.character(unlist(prefix[1]))
        if(length(prefix) > 1)
        {
            retval<-paste(paste(rep(extraPrefPerLevel, length(prefix) - 1), collapse=""), retval, sep="")
        }
        return(retval)
    }
}
This can be used in a logging function like this:
catw<-function(..., file = "", sep = " ", fill = FALSE, labels = NULL,
    append = FALSE, prefix=0)
{
    if(is.numeric(prefix))
    {
        prefix<-curfnfinder(skipframes=prefix+1) #note: the +1 is there to avoid returning catw itself
        prefix<-paste(prefix, ":", sep="")
    }
    cat(prefix, ..., format(Sys.time(), "(%Y-%m-%d %H:%M:%S)"), "\n",
        file = file, sep = sep, fill = fill, labels = labels, append = append)
}
As mentioned in the comments to Andrie's answer so far, there are still some issues regarding do.call. I'm going to stop spending time on it for now, but have posted the related question on the r-devel mailinglist. If/when I get a response there, and it is usable, I will update the functions.