They all mean "to encounter unexpectedly", but are used in different contexts:

Run into means to encounter someone (or something) during your normal course of events, often while physically traveling: I ran into Sally at the supermarket. Come across means to find something (or someone) when you were not looking for him/her/it: I was cleaning out the garage when I came across my high school yearbook.

Note that the phrase "come across" has a completely different sense where it also means "to be understood (perhaps wrongly)": I tried to tell her I was worried about her, but I'm afraid I came across as critical instead of concerned.

Come upon means to find a thing or (often) a situation during your course of events, somewhat similar to "run into" except usually referring to inanimate things or situations and without the implicit subcontext of physical travel: While reading Paradise Lost , I came upon the most amazing literary passage. It's often used interchangeably with "come across" (the first sense).

I disagree that "come upon" is now uncommon. It's never been an overly common expression, but I think it's probably used as much now as ever. --------------------------------------------------------

I will compare "run into" and "come across" in the meaning of "to meet something or someone". Those verbs have multiple meanings. "Come upon" is marked "literary" or "formal" in modern dictionaries. run into somebody (rather informal): meet someone you know by chance. The key word here is "someone you know". In this meaning, it doesn't have any negative connotations: I ran into an old neighbour of mine at the garage this afternoon. You rarely run into people you know in London. However, "run into something/someone" in the sense of "to crash (your vehicle) into it/them" is obviously bad. come across something: to find something unexpectedly when you are not looking for it but are doing something else, as in: Jill came across her son's diary when she was tidying his room one day. come across somebody: to meet/find someone by chance, when you are not expecting it, as in: You must have come across some weird and wonderful people while you were there. I came across an old school friend of mine when I was travelling in Canada.

I came across a group of children playing. He's the most unpleasant man I've ever come across. I came across children sleeping under bridges. My guess is that you usually run into people you know, whereas you come across people you know or total strangers. Also notice the following examples where "run into" doesn't sound good or it changes the meaning of a sentence: Just recently, I came across a familiar looking gorgeous man on facebook. Was just on a dating website and came across my ex girlfriend on it? Ever notice how you come across somebody once in a while you shouldn't have fucked with? Your [sic!] going to come across a lot of shitty bands, and a lot of shitty people. When you come across your crush, you feel like you are melting and as if you are going to faint. With things, it's simple. When you find something by chance, you come across it. The Oxford Phrasal Verbs Dictionary marks "come across sb/sth" as very common. It doesn't mark "run into" as common. Sources: the Longman Phrasal Verbs Dictionary, The Oxford Phrasal Verbs Dictionary, the Cambridge Phrasal Verbs Dictionary, the Longman Language Activator, The Oxford Learner's Thesaurus --------------------------------------------------------

In my experinece you run into people and trouble: I ran into Betty at the store today. I haven't seen her since college! I ran into your co-worker Bob today. Sorry I'm late; I ran into heavy traffic. You come across objects: I was cleaning up the kitchen and came across that phone bill you lost. I was looking up (something) in the encylopedia and came across this interesting tidbit.

come across

(v.) = encontrar por casualidad, encontrarse con, toparse con. Ex: In a jumble of old papers I recently came across the photograph of a young man striding through a classroom door.
come across2

(v.) = causar buena impresin.

Ex: Mr Berman, who is a very personable and enthusiastic librarian, certainly comes across.