I'd say you can skip most of SJA. The only episodes worth watching are those which have direct links to Doctor Who.
If you like the Slitheen, watch episodes 1 and 2 of Series 1, as well as episodes 9 and 10 of the same series. And possibly episodes 11 and 12 of Series 3, since I think they're featured.
If you like the Sontarans, watch episodes 1 and 2 of Series 2. Not a bad story, either.
If you like the Judoon, watch episodes 1 and 2 of Series 3.
Absolutely essential viewing, though, would be episodes 5 and 6 of Series 3. They're the episodes which David Tennant is in, and again, it's not a bad story. It also acts as a bit of a taster of what's to come in The Waters of Mars/The End of Time.
I think those are the only ones the have proper links to Doctor Who. K9 is also in a few episodes, though I'm not sure which. Possibly the final episodes of Series 1, and through most of Series 3.
It's not a great series, though. If Torchwood is made for adults, and Doctor Who is made for family viewing, then SJA is definitely made for kids. It shows on the children's BBC channel here, whilst Doctor Who and Torchwood don't. So it's all a bit simply and kiddy, and only worth watching to see Who characters appearing.
- Tilius