I'm reaonsably sympathetic to mobile phones - as long as the use is appropriate. 30 minute conversation - no. Business teleconference - no. Brief call to friend who's collecting you at the station, informing incoming callers that you're on the train but maintaining polite conversation for a couple of minutes - acceptable. Telling everyone about your toenail fungus... this should go without saying, but please no!
I'm also sympathetic to earphones
if and only if the person turns them down on request - I've politely asked a few times and had genuinely good results from people who don't realise that they're causing an intrusion to other passengers.
My pet peeve is blocking potentially usable seats. Feet on seats is a big no-no, and it happens everywhere (even First Class!). As for people who seem to kindly remove their shoes before placing their feet on the seats - I know what you're trying to do, but your feet frankly stink! Even worse than feet, though, is luggage. People often don't realise that most overhead luggage racks can take everything that an airline overhead bin can. So all hand luggage sized things can go in here. Instead, I frequently see overhead racks empty, but the exits to the carriages overflowing with large suitcases (as the small suitcases take up all usable space on the luggage rack).
Even more commonly, small bags blocking seats. I have on one occasion moved a suitcase to the overhead luggage rack rather forcibly as the woman opposite decided to take up a seat for her small suitcase when people were struggling to even board the train. I am still amazed that she didn't consider it appropriate to even try to make the seat available to a passenger, and that none of the other passengers/standees insisted that she move it! I'm also reminded of an instance where I commuted for a few days in a row on a specific service (Hyndland - Coatdyke, originating at Helensburgh). I'd get on the train and see a group of sheepish looking (mostly) men standing, whilst 16 perfectly good seats were taken up by 8 women (usually the same 8 women) and 8 strategically placed handbags. Every day I walked onto the train, asked one of them to move their bag. They did so, and that spurred other men to ask the same. It amazes me that, every day, despite getting on the train close to the end of the journey, I seemed to be the one who had to insist that I get a seat. Maybe I'm just not a gentleman
On the other side of the coin, I've seen someone who clearly has more cash than sense buying a ticket for her luggage so it could occupy the seat next to her(!). The staff on the (then) Virgin XC service were having none of it, pointed out that a ticket doesn't even entitle a person to a seat, and moved the bag to a luggage rack.