If you want to compare samples 1, 2, 3, and 4 and ask if any of them is different from control 1, then you should do a one-way analysis of variance (ANOVA). If you have a significant difference, you can then do a post hoc t-test (http://en.wikipedia.org/wiki/Student's_t-test) on each comparison (sample 1 vs. control 1, sample 2 vs. control 2, etc.) to see which differences were driving the effect.
You could also do individual t-tests on each (sample 1 vs. control 1, sample 2 vs control 1, etc) but if you do it that way you should correct for multiple comparisons. A pretty straightforward way to do this is using a Bonferroni correction, where you just divide you alpha-level by the number of comparisons you’re doing.
The same answer applies to your second question (comparing samples 1, 2, 3, and 4 against control 2).
Your third situation can be done with either a one-way ANOVA or a t-test; they will yield statistically identical results.
If you don’t have the software you need to do these comparisons send me a message and I will hook you up.