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I use tubes with screw caps and a rubber lining in the cap. For long-term storage it is advisable to keep these separate tubes in a larger jar with alcohol or do an annual check to see if alcohol levels are acceptable. The rubber lining may start to decay, so the caps should be checked as well to see if the need to be replaced.
Alternatively, you can use glass vials with cotton wool to close them and keep those in a larger jar with alcohol. Disadvantage of cotton wool may be that smaller flies get stuck in the cotton wool.
In general, I'd prefer glass over plastic even though glass, on average, will be more expensive. Plastic may degrade over time (burst) and glass may give enough visibility to examine specimens without having to take them out. Problems with the number of specimens only arise when there are really many of them in relation to tube size and when too much alcohol is in the tube. I store one species per tube, unless the specimens will not be identified (for example, all Sciaridae will go into one tube, all Cecidomyiidae, all Chloropidae, all Calyptrates, etc.).