I'll give you the answer I always give: it depends.
Combining everything into one file has many great benefits, including:
less network traffic - you might be retrieving one file, but you're sending/receiving multiple packets and each transaction has a series of SYN, SYN-ACK, and ACK messages sent across TCP. A large majority of the transfer time is establishing the session and there is a lot of overhead in the packet headers.
one location/manageability - although you may only have a few files, it's easy for functions (and class objects) to grow between versions. When you do the multiple file approach sometimes functions from one file call functions/objects from another file (ex. ajax in one file, then arithmetic functions in another - your arithmetic functions might grow to need to call the ajax and have a certain variable type returned). What ends up happening is that your set of files needs to be seen as one version, rather than each file being it's own version. Things get hairy down the road if you don't have good management in place and it's easy to fall out of line with Javascript files, which are always changing. Having one file makes it easy to manage the version between each of your pages across your (1 to many) websites.
Other topics to consider:
dormant code - you might think that the uncalled functions are potentially reducing performance by taking up space in memory and you'd be right, however this performance is so so so so minuscule, that it doesn't matter. Functions are indexed in memory and while the index table may increase, it's super trivial when dealing with small projects, especially given the hardware today.
memory leaks - this is probably the largest reason why you wouldn't want to combine all the code, however this is such a small issue given the amount of memory in systems today and the better garbage collection browsers have. Also, this is something that you, as a programmer, have the ability to control. Quality code leads to less problems like this.
Why it depends?
While it's easy to say throw all your code into one file, that would be wrong. It depends on how large your code is, how many functions, who maintains it, etc. Surely you wouldn't pack your locally written functions into the JQuery package and you may have different programmers that maintain different blocks of code - it depends on your setup.
It also depends on size. Some programmers embed the encoded images as ASCII in their files to reduce the number of files sent. These can bloat files. Surely you don't want to package everything into 1 50MB file. Especially if there are core functions that are needed for the page to load.
So to bring my response to a close, we'd need more information about your setup because it depends. Surely 3 files is acceptable regardless of size, combining where you would see fit. It probably wouldn't really hurt network traffic, but 50 files is more unreasonable. I use the hand rule (no more than 5), but surely you'll see a benefit combining those 5 1KB files into 1 5KB file.