I'm currently rewiring my basement and have done all the circuits but one. In an effort to save time/effort/money, I was wondering if it was possible to have a circuit with a 3-way switch that controlled lights BOTH between and at the end of the second switch?
From your question it sounds like you have a series of fixtures, some between the two switches and some past one of the switches. The key to a successful 3-way switch setup is maintaining the two traveler conductors between the two switches and then choosing one of the two switches as the "in" and the other as the "out".
Usually the "close" switch (the switch where either power comes direct from the breaker or where it comes from the first fixture) will have power and a neutral if it's fed from the breaker, but the distant switch will have just one 4 conductor wire running to it from the first switch, two travelers plus the hot return plus a ground. If you wanted to put more fixtures beyond that distant switch, you are missing the neutral.
My recommendation would be to find the "hot" point (where power first enters from the breaker) and identify the switched hot plus the neutral, and run standard 3-conductor from there to the additional fixtures. You might get lucky and find that where your fixtures need to go is closer to the "hot" point anyway. If not, sorry about your luck but it's time to buy some more romex!