Does your practice involve ashtanga-style sun salutations where you roll forward from a pushup position into upward-facing dog? If it does, make a big effort to be sure you're extending your ankles and rolling onto the tops of your arches rather than staying on your toes. If you don't normally practice upward-facing dog it might be worth trying - pay attention to what your feet are doing, but also be sure to keep the knees off the floor and avoid letting your lower back sag passively (dangerous)

Virasana without your butt on the floor is dangerous - too much knee strain. Sit on a cushion/block -- or -- sit *on* instead of *between* your heels. Either way, quite a good & safe ankle & knee opener. (Squatting - heels on the floor, feet as close together as you can get them while still keeping them reasonably parallel - is also a good knee opener, but more strain than supported virasana and does less for the ankles)

If you don't have big knee problems and can do half lotus safely, Marichyasana B is the ultimate ankle stretch.

(I had a hideous scary moment in Mysore, when I was in Marichyasana D for only about the second or third time and there was this *huge* ripping/crunching noise from my right ankle. Absolutely terrifying, thought I'd torn a ligament or something, but as it turned out it didn't hurt at all, just swelled a bit for a few days. I suspect some things that had calcified or otherwise stuck together had suddenly come un-stuck.)

PS: A good one for toes, that I learned in martial arts class rather than yoga, is kneeling with the knees apart about 90 degrees, balls of the feet on the floor and toes tucked under, butt on the heels. We had to do this for ages in the karate class I used to go to - hurts like hell for the first ten minutes or so.

Alan would have posted these suggestions as a comment but he was behind a firewall that did not permit him to do so.