This is a loaded question, but here are my 2 pennies....
Play a tone, play a note along side of it. If it sounds good, you are in tune.....simple ...RIGHT?
Yes, it is that simple. In the end, it is all about what sounds good.
There are a lot of factors that effect the pitch you hear....
1. You and the condition of your ears.
2. The environment.
3. Your playing volume.
4. The room.
You have to tune the instrument to the conditions. If I play with a group, I do not use a tuner, I tune to the group. If I pay with a Play-A-Long CD, I tune to the CD. If I play in the studio, I tune to the recording. Etc... Unless I am working on an instrument intonation adjustment, I NEVER use a tuner.
My suggestion is just listen to music, or the TV and start tuning to what you are listening to. When you play with others, have them play a note, try to match it, then ask them if it sounds ok to them. After a while, it will be second nature.