Crew management tips:
--- Names and saved positions
I like to rename my crew members to their preferred jobs. This helps me keep track of who is who and make sure the experience gained for each system is concentrated in a single character. Thus I'll have guys named Guns, Shields, Engines, Pilot, Fixer, Killer, Utility. With big crews, critical positions might be doubled up, so I might have a Guns1 and Guns2, for instance. I don't generally name crewman for positions that have no related skill, so I don't name guys "doors" or "sensors" for instance, but see two paragraphs down. I use the name "utility" for any crewman who will not be deliberately training in any specific skill.
Just renaming the guys isn't enough. Every time you add a new crew member or an old one dies, take a minute to reassess your standard crew layout, and move everybody where they will be the most effective at the start of a normal fight. Then click "save crew positions". With this done, at the end of each fight before jumping click "return crew to saved positions".
With a larger crew I try to always have a crewman whose saved position is the doors system; this is very helpful in boarding combat. Less crucial but useful is to have a guy stationed on the sensors system. The guys in these positions will be "fixers", "killers", or "utility", as there is no associated skill with doors or sensors. With doors and sensors covered, any extra guys will usually just get assigned saved positions to have fairly even coverage across the ship.
--- Racial preferences
When saving crew positions Zoltans should be placed in rooms that will consume energy. Weapons is first choice, shields second, engines third. Assigning a Zoltan anywhere else wastes his free energy ability. Systems can benefit from more than one Zoltan. Engi make the best fixers (damage repairers) but should avoid combat. Mantis make the best boarding combat guys (killers) with Rockmen generally second.
If you have 2 or more Lanius, consider making them your boarding combat team. Being able to evacuate a room's air and then send in Lanius to hurry along death by suffocation is sweet. If you have a mixed crew of Lanius and any other race on board, carefully segregate the Lanius so they never occupy the same room as the others.
The Slug telepathic abilities are great, and can often replace normal sensors, saving precious scrap for other systems. Best of all the telepathy works in nebulas! Anytime I get a Slug on board I carefully protect him.
I've never played with Crystal crew members so I can't offer much advice for them.
--- Crew acquisition
Whenever you fight a slaver ship. the "surrender offer" you get when the ship is nearly destroyed will be a free crewman. If you are short on crew this can be a great way to get new crew. If you have a pretty full crew or the crewman offered seems crappy, don't be shy about blowing the slaver to kingdom come and collecting that precious scrap. Yes, the poor suffering slaves they have on board will unfortunately die, but you must remember you are on a vital mission to save the Federation, and the needs of the many outweigh the needs of the few.
Occasionally you will get offered "reduced price" crewman by random encounters that cost some scrap but less than you would pay at a store. You will usually get offered enough free (or reduced price) crewman you don't need to buy a lot of them at stores, unless you have a habit of getting them killed. Paying full price at stores is pretty much last choice. One benefit of buying from stores is you usually get some choice about race, but only if you bring enough scrap to buy the spiffier races, and not just the bare minimum 45 for a human.
--- Experience management
I generally find getting experience for my weapons crewman (guns) goes much faster than other positions. Accumulated weapons experience is thus a bit less valuable than other types, since a new guy can pick it up quickly. Keep that in mind as you acquire new crewman. If your original weapons crewman is a race that might be more valuable for boarding or fixing (Mantis, Engi, Rockman) consider letting a new guy who doesn't have valuable racial advantages (or a Zoltan, who are GREAT on guns) take over the guns slot even though the original guy had some experience built up.
Acquiring experience for your pilot and engine crewmen can seem very slow. Keep in mind that experience for these positions depends on actually evading attacks. Powering engines may seem very low priority when assigning reactor bars, but keep in mind when you do this you are not only lowering your evasion chances you are also reducing the experience your pilot and engines guy will get. In order for these guys to max out experience by the final sector, make an effort to buy an extra engine bar or two early on and try to keep a couple of engine bars powered whenever possible, even if this means you take a bit more damage than you would if you spent the energy on something else like shields.
If you have a ship with a Zoltan shield, trying to concentrate shield experience in a shields guy is considerably less useful than in a normal ship. Shield experience depends on the shields actually blocking damage, but damage stopped by Zoltan shields does not add to experience. Furthermore the Zoltan shield gets no advantage from shield experience whatever. On a Zoltan shield equipped ship, crewing the shields position should be low priority, get a guy on weapons, pilot, engines, and maybe even doors before you bother assigning anyone to shields.
Killing enemy boarders by evacuating the rooms they are in and letting them suffocate is a time honored tactic that will fill your heart with glee. However, keep in mind that any boarder that suffocates to death is a boarder that died without anyone gaining experience for killing him. I like to do the suffocation trick to mostly, but not completely, kill boarders. When the poor saps get down to 25% health or so, I let them into a room with air, then send in my killers to mop up and soak up that lovely blood soaked experience.